From 6a5f96916bd7d11d1516885ebb81838de395ec58 Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Thu, 8 Feb 2024 10:11:06 +0000 Subject: [PATCH] Fix plot clustering clean scale, qc plot for mm10 --- config/config.yaml | 3 +- hs_err_pid2673469.log | 1323 + watchdog_pipeline/excluded_samples.yaml | 31 +- watchdog_pipeline/watchdog_pipeline.py | 1862 +- workflow/data/mm10.bin_200kb_all.bed | 27280 ++++++++-------- workflow/data/mm10.bin_200kb_all.bed.bak | 13640 ++++++++ workflow/rules/common.smk | 1 - workflow/rules/count.smk | 49 +- .../plotting/plot_clustering_dev_clean.R | 17 +- workflow/scripts/plotting/qc.R | 18 +- workflow/scripts/utils/update_counts.awk | 26 + 11 files changed, 29614 insertions(+), 14636 deletions(-) create mode 100644 hs_err_pid2673469.log create mode 100644 workflow/data/mm10.bin_200kb_all.bed.bak create mode 100644 workflow/scripts/utils/update_counts.awk diff --git a/config/config.yaml b/config/config.yaml index 30d2a317..f3b040c1 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -140,6 +140,7 @@ window: 200000 # Enable / Disable blacklisting of difficult mappable regions blacklist_regions: True +blacklist_regions_for_qc_plot: False # Enable or disable hand selection through the Jupyter Notebook hand_selection: False @@ -183,7 +184,7 @@ additional_sce_cutoff: 20000000 sce_min_distance: 500000 # Phasing parameters -snv_nb_threshold_for_strandphaser: 20 +snv_nb_threshold_for_strandphaser: 100 # -------------------------------------------------------- # Downstream modules configuration - genome browsing diff --git a/hs_err_pid2673469.log b/hs_err_pid2673469.log new file mode 100644 index 00000000..80d1195f --- /dev/null +++ b/hs_err_pid2673469.log @@ -0,0 +1,1323 @@ +# +# A fatal error has been detected by the Java Runtime Environment: +# +# SIGBUS (0x7) at pc=0x00007fffc971843e, pid=2673469, tid=2673703 +# +# JRE version: OpenJDK Runtime Environment (20.0.2) (build 20.0.2-internal-adhoc..src) +# Java VM: OpenJDK 64-Bit Server VM (20.0.2-internal-adhoc..src, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) +# Problematic frame: +# C [libfontconfig.so.1+0xb43e] FcDirCacheMapFd+0x33e +# +# Core dump will be written. Default location: Core dumps may be processed with "/usr/lib/systemd/systemd-coredump %P %u %g %s %t %c %h %e" (or dumping to /g/korbel2/weber/workspace/mosaicatcher-update/core.2673469) +# +# If you would like to submit a bug report, please visit: +# https://bugreport.java.com/bugreport/crash.jsp +# The crash happened outside the Java Virtual Machine in native code. +# See problematic frame for where to report the bug. +# + +--------------- S U M M A R Y ------------ + +Command Line: -Xms250m -Xmx250m -Dfastqc.output_dir=/scratch/jobs/46158308/tmpff74icft -Dfastqc.threads=1 -Dfastqc.quiet=true -XX:ParallelGCThreads=1 -Djava.awt.headless=true uk.ac.babraham.FastQC.FastQCApplication /scratch/tweber/DATA/MC_DATA/STOCKS/2024-01-30-AACT75KM5/HGSVCpool3NEWp2/fastq/HGSVCpool3NEWp2iTRUE11A33.2.fastq.gz + +Host: AMD EPYC 9754 128-Core Processor, 256 cores, 2G, Rocky Linux release 8.9 (Green Obsidian) +Time: Wed Jan 31 13:53:56 2024 CET elapsed time: 3.479508 seconds (0d 0h 0m 3s) + +--------------- T H R E A D --------------- + +Current thread (0x00007fff3c000e60): JavaThread "Thread-1" [_thread_in_native, id=2673703, stack(0x00007fffc9d07000,0x00007fffc9e08000)] + +Stack: [0x00007fffc9d07000,0x00007fffc9e08000], sp=0x00007fffc9e05700, free space=1017k +Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) +C [libfontconfig.so.1+0xb43e] FcDirCacheMapFd+0x33e +Java frames: (J=compiled Java code, j=interpreted, Vv=VM code) +j sun.font.FontConfigManager.getFontConfig(Ljava/lang/String;Lsun/font/FontConfigManager$FontConfigInfo;[Lsun/font/FontConfigManager$FcCompFont;Z)V+0 java.desktop@20.0.2-internal +j sun.font.FontConfigManager.initFontConfigFonts(Z)V+178 java.desktop@20.0.2-internal +j sun.font.FontConfigManager.loadFontConfig()[Lsun/font/FontConfigManager$FcCompFont;+2 java.desktop@20.0.2-internal +j sun.font.FcFontConfiguration.init()Z+39 java.desktop@20.0.2-internal +j sun.font.FcFontConfiguration.(Lsun/font/SunFontManager;)V+16 java.desktop@20.0.2-internal +j sun.awt.X11FontManager.createFontConfiguration()Lsun/awt/FontConfiguration;+27 java.desktop@20.0.2-internal +j sun.font.SunFontManager$2.run()Ljava/lang/Void;+206 java.desktop@20.0.2-internal +j sun.font.SunFontManager$2.run()Ljava/lang/Object;+1 java.desktop@20.0.2-internal +j java.security.AccessController.executePrivileged(Ljava/security/PrivilegedAction;Ljava/security/AccessControlContext;Ljava/lang/Class;)Ljava/lang/Object;+29 java.base@20.0.2-internal +j java.security.AccessController.doPrivileged(Ljava/security/PrivilegedAction;)Ljava/lang/Object;+5 java.base@20.0.2-internal +j sun.font.SunFontManager.()V+208 java.desktop@20.0.2-internal +j sun.awt.FcFontManager.()V+1 java.desktop@20.0.2-internal +j sun.awt.X11FontManager.()V+1 java.desktop@20.0.2-internal +j sun.font.PlatformFontInfo.createFontManager()Lsun/font/FontManager;+4 java.desktop@20.0.2-internal +j sun.font.FontManagerFactory.getInstance()Lsun/font/FontManager;+21 java.desktop@20.0.2-internal +j sun.font.SunFontManager.getInstance()Lsun/font/SunFontManager;+0 java.desktop@20.0.2-internal +j sun.font.FontDesignMetrics.getMetrics(Ljava/awt/Font;Ljava/awt/font/FontRenderContext;)Lsun/font/FontDesignMetrics;+0 java.desktop@20.0.2-internal +j sun.java2d.SunGraphics2D.getFontMetrics()Ljava/awt/FontMetrics;+21 java.desktop@20.0.2-internal +j uk.ac.babraham.FastQC.Graphs.QualityBoxPlot.paint(Ljava/awt/Graphics;)V+114 +j javax.swing.JComponent.print(Ljava/awt/Graphics;)V+18 java.desktop@20.0.2-internal +j uk.ac.babraham.FastQC.Modules.AbstractQCModule.writeDefaultImage(Luk/ac/babraham/FastQC/Report/HTMLReportArchive;Ljava/lang/String;Ljava/lang/String;II)V+100 +j uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.makeReport(Luk/ac/babraham/FastQC/Report/HTMLReportArchive;)V+34 +j uk.ac.babraham.FastQC.Report.HTMLReportArchive.(Luk/ac/babraham/FastQC/Sequence/SequenceFile;[Luk/ac/babraham/FastQC/Modules/QCModule;Ljava/io/File;)V+622 +j uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(Luk/ac/babraham/FastQC/Sequence/SequenceFile;[Luk/ac/babraham/FastQC/Modules/QCModule;)V+318 +j uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run()V+358 +j java.lang.Thread.runWith(Ljava/lang/Object;Ljava/lang/Runnable;)V+5 java.base@20.0.2-internal +j java.lang.Thread.run()V+19 java.base@20.0.2-internal +v ~StubRoutines::call_stub 0x00007fffe02eccc6 + +siginfo: si_signo: 7 (SIGBUS), si_code: 2 (BUS_ADRERR), si_addr: 0x00007ffff7e00000 + +Registers: +RAX=0x00007ffff7dfffff, RBX=0x0000000000002448, RCX=0x00007ffff7b2d44e, RDX=0x0000000000000000 +RSP=0x00007fffc9e05700, RBP=0x00007fff301bea00, RSI=0x0000000000000000, RDI=0x000000000000000c +R8 =0x000000000000000c, R9 =0x0000000000000000, R10=0x0000000000000003, R11=0x0000000000000246 +R12=0x00007fffc9e058b0, R13=0x000000000000000c, R14=0x00007fffc9e05820, R15=0x00007ffff7e00000 +RIP=0x00007fffc971843e, EFLAGS=0x0000000000010203, CSGSFS=0x002b000000000033, ERR=0x0000000000000004 + TRAPNO=0x000000000000000e + + +Register to memory mapping: + +RAX=0x00007ffff7dfffff is an unknown value +RBX=0x0000000000002448 is an unknown value +RCX=0x00007ffff7b2d44e: posix_fadvise+0x000000000000000e in /lib64/libc.so.6 at 0x00007ffff7a09000 +RDX=0x0 is NULL +RSP=0x00007fffc9e05700 is pointing into the stack for thread: 0x00007fff3c000e60 +RBP=0x00007fff301bea00 points into unknown readable memory: 0x00007fff301beab0 | b0 ea 1b 30 ff 7f 00 00 +RSI=0x0 is NULL +RDI=0x000000000000000c is an unknown value +R8 =0x000000000000000c is an unknown value +R9 =0x0 is NULL +R10=0x0000000000000003 is an unknown value +R11=0x0000000000000246 is an unknown value +R12=0x00007fffc9e058b0 is pointing into the stack for thread: 0x00007fff3c000e60 +R13=0x000000000000000c is an unknown value +R14=0x00007fffc9e05820 is pointing into the stack for thread: 0x00007fff3c000e60 +R15=0x00007ffff7e00000 is an unknown value + + +Top of Stack: (sp=0x00007fffc9e05700) +0x00007fffc9e05700: 00007fff302cf7f5 00007fffc9737263 +0x00007fffc9e05710: 000000000000002e 4ea4d1fe0049be00 +0x00007fffc9e05720: 00007fff301c26e0 00007fff30306460 +0x00007fffc9e05730: 00007fff300008d8 00007fffc9e057c0 +0x00007fffc9e05740: 00007fffc9e05750 4ea4d1fe0049be00 +0x00007fffc9e05750: 00000000000000b8 00007fffc9e05810 +0x00007fffc9e05760: 00007fffc9e058b0 00007fffc9e05820 +0x00007fffc9e05770: 00007fff302c72b0 00007fffc9e05a00 +0x00007fffc9e05780: 00007fff302cf750 00007fffc9718709 +0x00007fffc9e05790: 0000000000000000 00007fff301c5f20 +0x00007fffc9e057a0: 00007fff301bea00 00007fff302c72b0 +0x00007fffc9e057b0: 000000000000000c 00007fffc9717844 +0x00007fffc9e057c0: 0000000017389868 00007fff302c72d0 +0x00007fffc9e057d0: 0000000000000000 00007fffc9e05940 +0x00007fffc9e057e0: 00007fffc9e05a00 00007fffc9e05820 +0x00007fffc9e057f0: 0000000000000000 00007fffc97186f0 +0x00007fffc9e05800: 00007fffc9e058b0 00007fffc9e05810 +0x00007fffc9e05810: 0000000000000000 0000000000000000 +0x00007fffc9e05820: 0000000000000059 0000000000814a0a +0x00007fffc9e05830: 0000000000000001 00006285000081a4 +0x00007fffc9e05840: 00000000000003d6 0000000000000000 +0x00007fffc9e05850: 0000000000002448 0000000000100000 +0x00007fffc9e05860: 0000000000000018 0000000065ba42e4 +0x00007fffc9e05870: 0000000017849588 0000000065ba42e4 +0x00007fffc9e05880: 000000000f3c44c0 0000000065ba42e4 +0x00007fffc9e05890: 000000000f8874a8 0000000000000000 +0x00007fffc9e058a0: 0000000000000000 0000000000000000 +0x00007fffc9e058b0: 0000000000010303 0000000006112940 +0x00007fffc9e058c0: 0000000000000002 00000000000041ed +0x00007fffc9e058d0: 0000000000000000 0000000000000000 +0x00007fffc9e058e0: 0000000000000094 0000000000001000 +0x00007fffc9e058f0: 0000000000000000 0000000065ba026a + +Instructions: (pc=0x00007fffc971843e) +0x00007fffc971833e: 48 85 c0 79 c4 89 eb 0f 1f 00 85 db 0f 85 30 01 +0x00007fffc971834e: 00 00 49 8b 76 30 4c 89 ff ff 15 9b 0b 04 00 45 +0x00007fffc971835e: 31 ff 48 8b 44 24 48 64 48 2b 04 25 28 00 00 00 +0x00007fffc971836e: 0f 85 6a 03 00 00 48 83 c4 58 4c 89 f8 5b 5d 41 +0x00007fffc971837e: 5c 41 5d 41 5e 41 5f c3 66 2e 0f 1f 84 00 00 00 +0x00007fffc971838e: 00 00 48 8b 3d b1 0c 04 00 ff 15 03 0b 04 00 48 +0x00007fffc971839e: 8b 05 9c 0c 04 00 85 c0 0f 85 15 fe ff ff 48 8d +0x00007fffc97183ae: 3d 4b 5f 02 00 ff 15 47 08 04 00 48 85 c0 0f 84 +0x00007fffc97183be: cf 00 00 00 48 8d 74 24 3c 48 89 c7 e8 31 7a 01 +0x00007fffc97183ce: 00 85 c0 0f 84 ef 00 00 00 8b 44 24 3c 85 c0 0f +0x00007fffc97183de: 85 fe 00 00 00 48 c7 44 24 40 02 00 00 00 31 c0 +0x00007fffc97183ee: 48 8b 54 24 40 f0 48 0f b1 15 44 0c 04 00 49 8b +0x00007fffc97183fe: 5e 30 e9 e1 fd ff ff 45 31 c9 45 89 e8 b9 01 00 +0x00007fffc971840e: 00 00 ba 01 00 00 00 31 ff ff 15 7b 0a 04 00 49 +0x00007fffc971841e: 8b 56 30 b9 03 00 00 00 31 f6 49 89 c7 44 89 ef +0x00007fffc971842e: ff 15 5c 0b 04 00 49 8d 47 ff 48 83 f8 fd 77 76 +0x00007fffc971843e: 41 81 3f 04 fc 02 fc 49 8b 76 30 0f 85 05 ff ff +0x00007fffc971844e: ff 41 83 7f 04 07 0f 8e fa fe ff ff 4d 8b 47 08 +0x00007fffc971845e: 4c 39 c6 0f 85 ed fe ff ff 49 8b 47 10 31 db 48 +0x00007fffc971846e: 85 c0 0f 88 de fe ff ff e9 d0 fd ff ff 0f 1f 44 +0x00007fffc971847e: 00 00 4c 89 ff 45 31 ff ff 15 8c 07 04 00 e9 cf +0x00007fffc971848e: fe ff ff 48 c7 44 24 40 03 00 00 00 48 8b 54 24 +0x00007fffc971849e: 40 f0 48 0f b1 15 98 0b 04 00 44 89 ef e8 90 cb +0x00007fffc97184ae: 01 00 85 c0 75 09 49 8b 5e 30 e9 29 fd ff ff 49 +0x00007fffc97184be: 8b 76 30 e9 10 fd ff ff 48 c7 44 24 40 03 00 00 +0x00007fffc97184ce: 00 31 c0 48 8b 54 24 40 f0 48 0f b1 15 61 0b 04 +0x00007fffc97184de: 00 eb c7 48 c7 44 24 40 01 00 00 00 31 c0 48 8b +0x00007fffc97184ee: 54 24 40 f0 48 0f b1 15 46 0b 04 00 49 8b 76 30 +0x00007fffc97184fe: e9 d3 fc ff ff 4c 8b 44 24 28 89 eb 4c 89 e5 4d +0x00007fffc971850e: 89 ec 49 8b 4f 28 48 85 c9 0f 88 2b fe ff ff 4d +0x00007fffc971851e: 8d 48 f0 4c 39 c9 0f 87 1e fe ff ff 4c 01 f9 0f +0x00007fffc971852e: 84 65 01 00 00 4c 8b 54 24 08 48 63 31 48 bf ab + + +Stack slot to memory mapping: +stack at sp + 0 slots: 0x00007fff302cf7f5 points into unknown readable memory: 00 00 00 +stack at sp + 1 slots: 0x00007fffc9737263: FcStrBuildFilename+0x0000000000000113 in /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/../../libfontconfig.so.1 at 0x00007fffc970d000 +stack at sp + 2 slots: 0x000000000000002e is an unknown value +stack at sp + 3 slots: 0x4ea4d1fe0049be00 is an unknown value +stack at sp + 4 slots: 0x00007fff301c26e0 points into unknown readable memory: 0x00007ff8cfef2c82 | 82 2c ef cf f8 7f 00 00 +stack at sp + 5 slots: 0x00007fff30306460 points into unknown readable memory: 0x00007ff8cfe8fc66 | 66 fc e8 cf f8 7f 00 00 +stack at sp + 6 slots: 0x00007fff300008d8 points into unknown readable memory: 0x0007000100000007 | 07 00 00 00 01 00 07 00 +stack at sp + 7 slots: 0x00007fffc9e057c0 is pointing into the stack for thread: 0x00007fff3c000e60 + + +--------------- P R O C E S S --------------- + +Threads class SMR info: +_java_thread_list=0x00007fff300f1b50, length=13, elements={ +0x00007ffff00195d0, 0x00007ffff015a050, 0x00007ffff015b5b0, 0x00007ffff015cf50, +0x00007ffff015e3e0, 0x00007ffff015f860, 0x00007ffff0161280, 0x00007ffff0162820, +0x00007ffff01791d0, 0x00007ffff017d980, 0x00007ffff0242360, 0x00007fff3c000e60, +0x00007fff300f0d80 +} + +Java Threads: ( => current thread ) + 0x00007ffff00195d0 JavaThread "main" [_thread_blocked, id=2673517, stack(0x00007ffff7ea6000,0x00007ffff7fa7000)] + 0x00007ffff015a050 JavaThread "Reference Handler" daemon [_thread_blocked, id=2673570, stack(0x00007fffd895d000,0x00007fffd8a5e000)] + 0x00007ffff015b5b0 JavaThread "Finalizer" daemon [_thread_blocked, id=2673572, stack(0x00007fffd885c000,0x00007fffd895d000)] + 0x00007ffff015cf50 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=2673574, stack(0x00007fffd875b000,0x00007fffd885c000)] + 0x00007ffff015e3e0 JavaThread "Service Thread" daemon [_thread_blocked, id=2673575, stack(0x00007fffd865a000,0x00007fffd875b000)] + 0x00007ffff015f860 JavaThread "Monitor Deflation Thread" daemon [_thread_blocked, id=2673577, stack(0x00007fffd8559000,0x00007fffd865a000)] + 0x00007ffff0161280 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=2673579, stack(0x00007fffd8458000,0x00007fffd8559000)] + 0x00007ffff0162820 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=2673581, stack(0x00007fffd8357000,0x00007fffd8458000)] + 0x00007ffff01791d0 JavaThread "Notification Thread" daemon [_thread_blocked, id=2673584, stack(0x00007fffd8256000,0x00007fffd8357000)] + 0x00007ffff017d980 JavaThread "Common-Cleaner" daemon [_thread_blocked, id=2673589, stack(0x00007fffd8053000,0x00007fffd8154000)] + 0x00007ffff0242360 JavaThread "Thread-0" [_thread_blocked, id=2673701, stack(0x00007fffc9e08000,0x00007fffc9f09000)] +=>0x00007fff3c000e60 JavaThread "Thread-1" [_thread_in_native, id=2673703, stack(0x00007fffc9d07000,0x00007fffc9e08000)] + 0x00007fff300f0d80 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=2674599, stack(0x00007fffc9c06000,0x00007fffc9d07000)] + +Other Threads: + 0x00007ffff014d520 VMThread "VM Thread" [stack: 0x00007fffd8a60000,0x00007fffd8b60000] [id=2673568] + 0x00007ffff017afc0 WatcherThread "VM Periodic Task Thread" [stack: 0x00007fffd8156000,0x00007fffd8256000] [id=2673586] + 0x00007ffff0042ad0 WorkerThread "GC Thread#0" [stack: 0x00007ffff450a000,0x00007ffff460a000] [id=2673537] + 0x00007ffff0045fc0 ConcurrentGCThread "G1 Main Marker" [stack: 0x00007ffff4408000,0x00007ffff4508000] [id=2673539] + 0x00007ffff0046ee0 WorkerThread "G1 Conc#0" [stack: 0x00007ffff4306000,0x00007ffff4406000] [id=2673541] + 0x00007ffff011e190 ConcurrentGCThread "G1 Refine#0" [stack: 0x00007ffff4103000,0x00007ffff4203000] [id=2673543] + 0x00007ffff011f0d0 ConcurrentGCThread "G1 Service" [stack: 0x00007fffd8cb4000,0x00007fffd8db4000] [id=2673544] + +Threads with active compile tasks: + +VM state: not at safepoint (normal execution) + +VM Mutex/Monitor currently owned by a thread: None + +Heap address: 0x00000000f0600000, size: 250 MB, Compressed Oops mode: 32-bit + +CDS archive(s) mapped at: [0x00007fff7b000000-0x00007fff7bc6f000-0x00007fff7bc6f000), size 13037568, SharedBaseAddress: 0x00007fff7b000000, ArchiveRelocationMode: 1. +Compressed class space mapped at: 0x00007fff7c000000-0x00007fffbc000000, reserved size: 1073741824 +Narrow klass base: 0x00007fff7b000000, Narrow klass shift: 0, Narrow klass range: 0x100000000 + +GC Precious Log: + CardTable entry size: 512 + Card Set container configuration: InlinePtr #cards 5 size 8 Array Of Cards #cards 12 size 40 Howl #buckets 4 coarsen threshold 1843 Howl Bitmap #cards 512 size 80 coarsen threshold 460 Card regions per heap region 1 cards per card region 2048 + CPUs: 256 total, 2 available + Memory: 2200M + Large Page Support: Disabled + NUMA Support: Disabled + Compressed Oops: Enabled (32-bit) + Heap Region Size: 1M + Heap Min Capacity: 250M + Heap Initial Capacity: 250M + Heap Max Capacity: 250M + Pre-touch: Disabled + Parallel Workers: 1 + Concurrent Workers: 1 + Concurrent Refinement Workers: 1 + Periodic GC: Disabled + +Heap: + garbage-first heap total 256000K, used 115696K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 83 young (84992K), 5 survivors (5120K) + Metaspace used 7539K, committed 7808K, reserved 1114112K + class space used 772K, committed 896K, reserved 1048576K + +Heap Regions: E=young(eden), S=young(survivor), O=old, HS=humongous(starts), HC=humongous(continues), CS=collection set, F=free, OA=open archive, CA=closed archive, TAMS=top-at-mark-start, PB=parsable bottom +| 0|0x00000000f0600000, 0x00000000f0700000, 0x00000000f0700000|100%| O| |TAMS 0x00000000f0600000| PB 0x00000000f0600000| Untracked +| 1|0x00000000f0700000, 0x00000000f0800000, 0x00000000f0800000|100%| O| |TAMS 0x00000000f0700000| PB 0x00000000f0700000| Untracked +| 2|0x00000000f0800000, 0x00000000f0900000, 0x00000000f0900000|100%| O| |TAMS 0x00000000f0800000| PB 0x00000000f0800000| Untracked +| 3|0x00000000f0900000, 0x00000000f0a00000, 0x00000000f0a00000|100%| O| |TAMS 0x00000000f0900000| PB 0x00000000f0900000| Untracked +| 4|0x00000000f0a00000, 0x00000000f0b00000, 0x00000000f0b00000|100%| O| |TAMS 0x00000000f0a00000| PB 0x00000000f0a00000| Untracked +| 5|0x00000000f0b00000, 0x00000000f0c00000, 0x00000000f0c00000|100%| O| |TAMS 0x00000000f0b00000| PB 0x00000000f0b00000| Untracked +| 6|0x00000000f0c00000, 0x00000000f0d00000, 0x00000000f0d00000|100%| O| |TAMS 0x00000000f0c00000| PB 0x00000000f0c00000| Untracked +| 7|0x00000000f0d00000, 0x00000000f0e00000, 0x00000000f0e00000|100%| O| |TAMS 0x00000000f0d00000| PB 0x00000000f0d00000| Untracked +| 8|0x00000000f0e00000, 0x00000000f0f00000, 0x00000000f0f00000|100%| O| |TAMS 0x00000000f0e00000| PB 0x00000000f0e00000| Untracked +| 9|0x00000000f0f00000, 0x00000000f1000000, 0x00000000f1000000|100%| O| |TAMS 0x00000000f0f00000| PB 0x00000000f0f00000| Untracked +| 10|0x00000000f1000000, 0x00000000f1100000, 0x00000000f1100000|100%| O| |TAMS 0x00000000f1000000| PB 0x00000000f1000000| Untracked +| 11|0x00000000f1100000, 0x00000000f1200000, 0x00000000f1200000|100%| O| |TAMS 0x00000000f1100000| PB 0x00000000f1100000| Untracked +| 12|0x00000000f1200000, 0x00000000f1300000, 0x00000000f1300000|100%| O| |TAMS 0x00000000f1200000| PB 0x00000000f1200000| Untracked +| 13|0x00000000f1300000, 0x00000000f1400000, 0x00000000f1400000|100%| O| |TAMS 0x00000000f1300000| PB 0x00000000f1300000| Untracked +| 14|0x00000000f1400000, 0x00000000f1500000, 0x00000000f1500000|100%| O| |TAMS 0x00000000f1400000| PB 0x00000000f1400000| Untracked +| 15|0x00000000f1500000, 0x00000000f1600000, 0x00000000f1600000|100%| O| |TAMS 0x00000000f1500000| PB 0x00000000f1500000| Untracked +| 16|0x00000000f1600000, 0x00000000f1700000, 0x00000000f1700000|100%| O| |TAMS 0x00000000f1600000| PB 0x00000000f1600000| Untracked +| 17|0x00000000f1700000, 0x00000000f1800000, 0x00000000f1800000|100%| O| |TAMS 0x00000000f1700000| PB 0x00000000f1700000| Untracked +| 18|0x00000000f1800000, 0x00000000f1900000, 0x00000000f1900000|100%| O| |TAMS 0x00000000f1800000| PB 0x00000000f1800000| Untracked +| 19|0x00000000f1900000, 0x00000000f1a00000, 0x00000000f1a00000|100%| O| |TAMS 0x00000000f1900000| PB 0x00000000f1900000| Untracked +| 20|0x00000000f1a00000, 0x00000000f1b00000, 0x00000000f1b00000|100%| O| |TAMS 0x00000000f1a00000| PB 0x00000000f1a00000| Untracked +| 21|0x00000000f1b00000, 0x00000000f1c00000, 0x00000000f1c00000|100%| O| |TAMS 0x00000000f1b00000| PB 0x00000000f1b00000| Untracked +| 22|0x00000000f1c00000, 0x00000000f1d00000, 0x00000000f1d00000|100%| O| |TAMS 0x00000000f1c00000| PB 0x00000000f1c00000| Untracked +| 23|0x00000000f1d00000, 0x00000000f1e00000, 0x00000000f1e00000|100%| O| |TAMS 0x00000000f1d00000| PB 0x00000000f1d00000| Untracked +| 24|0x00000000f1e00000, 0x00000000f1f00000, 0x00000000f1f00000|100%| O| |TAMS 0x00000000f1e00000| PB 0x00000000f1e00000| Untracked +| 25|0x00000000f1f00000, 0x00000000f2000000, 0x00000000f2000000|100%| O| |TAMS 0x00000000f1f00000| PB 0x00000000f1f00000| Untracked +| 26|0x00000000f2000000, 0x00000000f2100000, 0x00000000f2100000|100%| O| |TAMS 0x00000000f2000000| PB 0x00000000f2000000| Untracked +| 27|0x00000000f2100000, 0x00000000f2200000, 0x00000000f2200000|100%|HS| |TAMS 0x00000000f2100000| PB 0x00000000f2100000| Complete +| 28|0x00000000f2200000, 0x00000000f2300000, 0x00000000f2300000|100%|HC| |TAMS 0x00000000f2200000| PB 0x00000000f2200000| Complete +| 29|0x00000000f2300000, 0x00000000f2400000, 0x00000000f2400000|100%|HC| |TAMS 0x00000000f2300000| PB 0x00000000f2300000| Complete +| 30|0x00000000f2400000, 0x00000000f2400000, 0x00000000f2500000| 0%| F| |TAMS 0x00000000f2400000| PB 0x00000000f2400000| Untracked +| 31|0x00000000f2500000, 0x00000000f2500000, 0x00000000f2600000| 0%| F| |TAMS 0x00000000f2500000| PB 0x00000000f2500000| Untracked +| 32|0x00000000f2600000, 0x00000000f2600000, 0x00000000f2700000| 0%| F| |TAMS 0x00000000f2600000| PB 0x00000000f2600000| Untracked +| 33|0x00000000f2700000, 0x00000000f2700000, 0x00000000f2800000| 0%| F| |TAMS 0x00000000f2700000| PB 0x00000000f2700000| Untracked +| 34|0x00000000f2800000, 0x00000000f2800000, 0x00000000f2900000| 0%| F| |TAMS 0x00000000f2800000| PB 0x00000000f2800000| Untracked +| 35|0x00000000f2900000, 0x00000000f2900000, 0x00000000f2a00000| 0%| F| |TAMS 0x00000000f2900000| PB 0x00000000f2900000| Untracked +| 36|0x00000000f2a00000, 0x00000000f2a00000, 0x00000000f2b00000| 0%| F| |TAMS 0x00000000f2a00000| PB 0x00000000f2a00000| Untracked +| 37|0x00000000f2b00000, 0x00000000f2b00000, 0x00000000f2c00000| 0%| F| |TAMS 0x00000000f2b00000| PB 0x00000000f2b00000| Untracked +| 38|0x00000000f2c00000, 0x00000000f2c00000, 0x00000000f2d00000| 0%| F| |TAMS 0x00000000f2c00000| PB 0x00000000f2c00000| Untracked +| 39|0x00000000f2d00000, 0x00000000f2d00000, 0x00000000f2e00000| 0%| F| |TAMS 0x00000000f2d00000| PB 0x00000000f2d00000| Untracked +| 40|0x00000000f2e00000, 0x00000000f2e00000, 0x00000000f2f00000| 0%| F| |TAMS 0x00000000f2e00000| PB 0x00000000f2e00000| Untracked +| 41|0x00000000f2f00000, 0x00000000f2f00000, 0x00000000f3000000| 0%| F| |TAMS 0x00000000f2f00000| PB 0x00000000f2f00000| Untracked +| 42|0x00000000f3000000, 0x00000000f3000000, 0x00000000f3100000| 0%| F| |TAMS 0x00000000f3000000| PB 0x00000000f3000000| Untracked +| 43|0x00000000f3100000, 0x00000000f3100000, 0x00000000f3200000| 0%| F| |TAMS 0x00000000f3100000| PB 0x00000000f3100000| Untracked +| 44|0x00000000f3200000, 0x00000000f3200000, 0x00000000f3300000| 0%| F| |TAMS 0x00000000f3200000| PB 0x00000000f3200000| Untracked +| 45|0x00000000f3300000, 0x00000000f3300000, 0x00000000f3400000| 0%| F| |TAMS 0x00000000f3300000| PB 0x00000000f3300000| Untracked +| 46|0x00000000f3400000, 0x00000000f3400000, 0x00000000f3500000| 0%| F| |TAMS 0x00000000f3400000| PB 0x00000000f3400000| Untracked +| 47|0x00000000f3500000, 0x00000000f3500000, 0x00000000f3600000| 0%| F| |TAMS 0x00000000f3500000| PB 0x00000000f3500000| Untracked +| 48|0x00000000f3600000, 0x00000000f3600000, 0x00000000f3700000| 0%| F| |TAMS 0x00000000f3600000| PB 0x00000000f3600000| Untracked +| 49|0x00000000f3700000, 0x00000000f3700000, 0x00000000f3800000| 0%| F| |TAMS 0x00000000f3700000| PB 0x00000000f3700000| Untracked +| 50|0x00000000f3800000, 0x00000000f3800000, 0x00000000f3900000| 0%| F| |TAMS 0x00000000f3800000| PB 0x00000000f3800000| Untracked +| 51|0x00000000f3900000, 0x00000000f3900000, 0x00000000f3a00000| 0%| F| |TAMS 0x00000000f3900000| PB 0x00000000f3900000| Untracked +| 52|0x00000000f3a00000, 0x00000000f3a00000, 0x00000000f3b00000| 0%| F| |TAMS 0x00000000f3a00000| PB 0x00000000f3a00000| Untracked +| 53|0x00000000f3b00000, 0x00000000f3b00000, 0x00000000f3c00000| 0%| F| |TAMS 0x00000000f3b00000| PB 0x00000000f3b00000| Untracked +| 54|0x00000000f3c00000, 0x00000000f3c00000, 0x00000000f3d00000| 0%| F| |TAMS 0x00000000f3c00000| PB 0x00000000f3c00000| Untracked +| 55|0x00000000f3d00000, 0x00000000f3d00000, 0x00000000f3e00000| 0%| F| |TAMS 0x00000000f3d00000| PB 0x00000000f3d00000| Untracked +| 56|0x00000000f3e00000, 0x00000000f3e00000, 0x00000000f3f00000| 0%| F| |TAMS 0x00000000f3e00000| PB 0x00000000f3e00000| Untracked +| 57|0x00000000f3f00000, 0x00000000f3f00000, 0x00000000f4000000| 0%| F| |TAMS 0x00000000f3f00000| PB 0x00000000f3f00000| Untracked +| 58|0x00000000f4000000, 0x00000000f4000000, 0x00000000f4100000| 0%| F| |TAMS 0x00000000f4000000| PB 0x00000000f4000000| Untracked +| 59|0x00000000f4100000, 0x00000000f4100000, 0x00000000f4200000| 0%| F| |TAMS 0x00000000f4100000| PB 0x00000000f4100000| Untracked +| 60|0x00000000f4200000, 0x00000000f4200000, 0x00000000f4300000| 0%| F| |TAMS 0x00000000f4200000| PB 0x00000000f4200000| Untracked +| 61|0x00000000f4300000, 0x00000000f4300000, 0x00000000f4400000| 0%| F| |TAMS 0x00000000f4300000| PB 0x00000000f4300000| Untracked +| 62|0x00000000f4400000, 0x00000000f4400000, 0x00000000f4500000| 0%| F| |TAMS 0x00000000f4400000| PB 0x00000000f4400000| Untracked +| 63|0x00000000f4500000, 0x00000000f4500000, 0x00000000f4600000| 0%| F| |TAMS 0x00000000f4500000| PB 0x00000000f4500000| Untracked +| 64|0x00000000f4600000, 0x00000000f4600000, 0x00000000f4700000| 0%| F| |TAMS 0x00000000f4600000| PB 0x00000000f4600000| Untracked +| 65|0x00000000f4700000, 0x00000000f4700000, 0x00000000f4800000| 0%| F| |TAMS 0x00000000f4700000| PB 0x00000000f4700000| Untracked +| 66|0x00000000f4800000, 0x00000000f4800000, 0x00000000f4900000| 0%| F| |TAMS 0x00000000f4800000| PB 0x00000000f4800000| Untracked +| 67|0x00000000f4900000, 0x00000000f4900000, 0x00000000f4a00000| 0%| F| |TAMS 0x00000000f4900000| PB 0x00000000f4900000| Untracked +| 68|0x00000000f4a00000, 0x00000000f4a00000, 0x00000000f4b00000| 0%| F| |TAMS 0x00000000f4a00000| PB 0x00000000f4a00000| Untracked +| 69|0x00000000f4b00000, 0x00000000f4b00000, 0x00000000f4c00000| 0%| F| |TAMS 0x00000000f4b00000| PB 0x00000000f4b00000| Untracked +| 70|0x00000000f4c00000, 0x00000000f4c00000, 0x00000000f4d00000| 0%| F| |TAMS 0x00000000f4c00000| PB 0x00000000f4c00000| Untracked +| 71|0x00000000f4d00000, 0x00000000f4d00000, 0x00000000f4e00000| 0%| F| |TAMS 0x00000000f4d00000| PB 0x00000000f4d00000| Untracked +| 72|0x00000000f4e00000, 0x00000000f4e00000, 0x00000000f4f00000| 0%| F| |TAMS 0x00000000f4e00000| PB 0x00000000f4e00000| Untracked +| 73|0x00000000f4f00000, 0x00000000f4f00000, 0x00000000f5000000| 0%| F| |TAMS 0x00000000f4f00000| PB 0x00000000f4f00000| Untracked +| 74|0x00000000f5000000, 0x00000000f5000000, 0x00000000f5100000| 0%| F| |TAMS 0x00000000f5000000| PB 0x00000000f5000000| Untracked +| 75|0x00000000f5100000, 0x00000000f5100000, 0x00000000f5200000| 0%| F| |TAMS 0x00000000f5100000| PB 0x00000000f5100000| Untracked +| 76|0x00000000f5200000, 0x00000000f5200000, 0x00000000f5300000| 0%| F| |TAMS 0x00000000f5200000| PB 0x00000000f5200000| Untracked +| 77|0x00000000f5300000, 0x00000000f5300000, 0x00000000f5400000| 0%| F| |TAMS 0x00000000f5300000| PB 0x00000000f5300000| Untracked +| 78|0x00000000f5400000, 0x00000000f5400000, 0x00000000f5500000| 0%| F| |TAMS 0x00000000f5400000| PB 0x00000000f5400000| Untracked +| 79|0x00000000f5500000, 0x00000000f5500000, 0x00000000f5600000| 0%| F| |TAMS 0x00000000f5500000| PB 0x00000000f5500000| Untracked +| 80|0x00000000f5600000, 0x00000000f5600000, 0x00000000f5700000| 0%| F| |TAMS 0x00000000f5600000| PB 0x00000000f5600000| Untracked +| 81|0x00000000f5700000, 0x00000000f5700000, 0x00000000f5800000| 0%| F| |TAMS 0x00000000f5700000| PB 0x00000000f5700000| Untracked +| 82|0x00000000f5800000, 0x00000000f5800000, 0x00000000f5900000| 0%| F| |TAMS 0x00000000f5800000| PB 0x00000000f5800000| Untracked +| 83|0x00000000f5900000, 0x00000000f5900000, 0x00000000f5a00000| 0%| F| |TAMS 0x00000000f5900000| PB 0x00000000f5900000| Untracked +| 84|0x00000000f5a00000, 0x00000000f5a00000, 0x00000000f5b00000| 0%| F| |TAMS 0x00000000f5a00000| PB 0x00000000f5a00000| Untracked +| 85|0x00000000f5b00000, 0x00000000f5b00000, 0x00000000f5c00000| 0%| F| |TAMS 0x00000000f5b00000| PB 0x00000000f5b00000| Untracked +| 86|0x00000000f5c00000, 0x00000000f5c00000, 0x00000000f5d00000| 0%| F| |TAMS 0x00000000f5c00000| PB 0x00000000f5c00000| Untracked +| 87|0x00000000f5d00000, 0x00000000f5d00000, 0x00000000f5e00000| 0%| F| |TAMS 0x00000000f5d00000| PB 0x00000000f5d00000| Untracked +| 88|0x00000000f5e00000, 0x00000000f5e00000, 0x00000000f5f00000| 0%| F| |TAMS 0x00000000f5e00000| PB 0x00000000f5e00000| Untracked +| 89|0x00000000f5f00000, 0x00000000f5f00000, 0x00000000f6000000| 0%| F| |TAMS 0x00000000f5f00000| PB 0x00000000f5f00000| Untracked +| 90|0x00000000f6000000, 0x00000000f6000000, 0x00000000f6100000| 0%| F| |TAMS 0x00000000f6000000| PB 0x00000000f6000000| Untracked +| 91|0x00000000f6100000, 0x00000000f6100000, 0x00000000f6200000| 0%| F| |TAMS 0x00000000f6100000| PB 0x00000000f6100000| Untracked +| 92|0x00000000f6200000, 0x00000000f6200000, 0x00000000f6300000| 0%| F| |TAMS 0x00000000f6200000| PB 0x00000000f6200000| Untracked +| 93|0x00000000f6300000, 0x00000000f6300000, 0x00000000f6400000| 0%| F| |TAMS 0x00000000f6300000| PB 0x00000000f6300000| Untracked +| 94|0x00000000f6400000, 0x00000000f6400000, 0x00000000f6500000| 0%| F| |TAMS 0x00000000f6400000| PB 0x00000000f6400000| Untracked +| 95|0x00000000f6500000, 0x00000000f6500000, 0x00000000f6600000| 0%| F| |TAMS 0x00000000f6500000| PB 0x00000000f6500000| Untracked +| 96|0x00000000f6600000, 0x00000000f6600000, 0x00000000f6700000| 0%| F| |TAMS 0x00000000f6600000| PB 0x00000000f6600000| Untracked +| 97|0x00000000f6700000, 0x00000000f6700000, 0x00000000f6800000| 0%| F| |TAMS 0x00000000f6700000| PB 0x00000000f6700000| Untracked +| 98|0x00000000f6800000, 0x00000000f6800000, 0x00000000f6900000| 0%| F| |TAMS 0x00000000f6800000| PB 0x00000000f6800000| Untracked +| 99|0x00000000f6900000, 0x00000000f6900000, 0x00000000f6a00000| 0%| F| |TAMS 0x00000000f6900000| PB 0x00000000f6900000| Untracked +| 100|0x00000000f6a00000, 0x00000000f6a00000, 0x00000000f6b00000| 0%| F| |TAMS 0x00000000f6a00000| PB 0x00000000f6a00000| Untracked +| 101|0x00000000f6b00000, 0x00000000f6b00000, 0x00000000f6c00000| 0%| F| |TAMS 0x00000000f6b00000| PB 0x00000000f6b00000| Untracked +| 102|0x00000000f6c00000, 0x00000000f6c00000, 0x00000000f6d00000| 0%| F| |TAMS 0x00000000f6c00000| PB 0x00000000f6c00000| Untracked +| 103|0x00000000f6d00000, 0x00000000f6d00000, 0x00000000f6e00000| 0%| F| |TAMS 0x00000000f6d00000| PB 0x00000000f6d00000| Untracked +| 104|0x00000000f6e00000, 0x00000000f6e00000, 0x00000000f6f00000| 0%| F| |TAMS 0x00000000f6e00000| PB 0x00000000f6e00000| Untracked +| 105|0x00000000f6f00000, 0x00000000f6f00000, 0x00000000f7000000| 0%| F| |TAMS 0x00000000f6f00000| PB 0x00000000f6f00000| Untracked +| 106|0x00000000f7000000, 0x00000000f7000000, 0x00000000f7100000| 0%| F| |TAMS 0x00000000f7000000| PB 0x00000000f7000000| Untracked +| 107|0x00000000f7100000, 0x00000000f7100000, 0x00000000f7200000| 0%| F| |TAMS 0x00000000f7100000| PB 0x00000000f7100000| Untracked +| 108|0x00000000f7200000, 0x00000000f7200000, 0x00000000f7300000| 0%| F| |TAMS 0x00000000f7200000| PB 0x00000000f7200000| Untracked +| 109|0x00000000f7300000, 0x00000000f7300000, 0x00000000f7400000| 0%| F| |TAMS 0x00000000f7300000| PB 0x00000000f7300000| Untracked +| 110|0x00000000f7400000, 0x00000000f7400000, 0x00000000f7500000| 0%| F| |TAMS 0x00000000f7400000| PB 0x00000000f7400000| Untracked +| 111|0x00000000f7500000, 0x00000000f7500000, 0x00000000f7600000| 0%| F| |TAMS 0x00000000f7500000| PB 0x00000000f7500000| Untracked +| 112|0x00000000f7600000, 0x00000000f7600000, 0x00000000f7700000| 0%| F| |TAMS 0x00000000f7600000| PB 0x00000000f7600000| Untracked +| 113|0x00000000f7700000, 0x00000000f7700000, 0x00000000f7800000| 0%| F| |TAMS 0x00000000f7700000| PB 0x00000000f7700000| Untracked +| 114|0x00000000f7800000, 0x00000000f7800000, 0x00000000f7900000| 0%| F| |TAMS 0x00000000f7800000| PB 0x00000000f7800000| Untracked +| 115|0x00000000f7900000, 0x00000000f7900000, 0x00000000f7a00000| 0%| F| |TAMS 0x00000000f7900000| PB 0x00000000f7900000| Untracked +| 116|0x00000000f7a00000, 0x00000000f7a00000, 0x00000000f7b00000| 0%| F| |TAMS 0x00000000f7a00000| PB 0x00000000f7a00000| Untracked +| 117|0x00000000f7b00000, 0x00000000f7b00000, 0x00000000f7c00000| 0%| F| |TAMS 0x00000000f7b00000| PB 0x00000000f7b00000| Untracked +| 118|0x00000000f7c00000, 0x00000000f7c00000, 0x00000000f7d00000| 0%| F| |TAMS 0x00000000f7c00000| PB 0x00000000f7c00000| Untracked +| 119|0x00000000f7d00000, 0x00000000f7d00000, 0x00000000f7e00000| 0%| F| |TAMS 0x00000000f7d00000| PB 0x00000000f7d00000| Untracked +| 120|0x00000000f7e00000, 0x00000000f7e00000, 0x00000000f7f00000| 0%| F| |TAMS 0x00000000f7e00000| PB 0x00000000f7e00000| Untracked +| 121|0x00000000f7f00000, 0x00000000f7f00000, 0x00000000f8000000| 0%| F| |TAMS 0x00000000f7f00000| PB 0x00000000f7f00000| Untracked +| 122|0x00000000f8000000, 0x00000000f8000000, 0x00000000f8100000| 0%| F| |TAMS 0x00000000f8000000| PB 0x00000000f8000000| Untracked +| 123|0x00000000f8100000, 0x00000000f8100000, 0x00000000f8200000| 0%| F| |TAMS 0x00000000f8100000| PB 0x00000000f8100000| Untracked +| 124|0x00000000f8200000, 0x00000000f8200000, 0x00000000f8300000| 0%| F| |TAMS 0x00000000f8200000| PB 0x00000000f8200000| Untracked +| 125|0x00000000f8300000, 0x00000000f8300000, 0x00000000f8400000| 0%| F| |TAMS 0x00000000f8300000| PB 0x00000000f8300000| Untracked +| 126|0x00000000f8400000, 0x00000000f8400000, 0x00000000f8500000| 0%| F| |TAMS 0x00000000f8400000| PB 0x00000000f8400000| Untracked +| 127|0x00000000f8500000, 0x00000000f8500000, 0x00000000f8600000| 0%| F| |TAMS 0x00000000f8500000| PB 0x00000000f8500000| Untracked +| 128|0x00000000f8600000, 0x00000000f8600000, 0x00000000f8700000| 0%| F| |TAMS 0x00000000f8600000| PB 0x00000000f8600000| Untracked +| 129|0x00000000f8700000, 0x00000000f8700000, 0x00000000f8800000| 0%| F| |TAMS 0x00000000f8700000| PB 0x00000000f8700000| Untracked +| 130|0x00000000f8800000, 0x00000000f8800000, 0x00000000f8900000| 0%| F| |TAMS 0x00000000f8800000| PB 0x00000000f8800000| Untracked +| 131|0x00000000f8900000, 0x00000000f8900000, 0x00000000f8a00000| 0%| F| |TAMS 0x00000000f8900000| PB 0x00000000f8900000| Untracked +| 132|0x00000000f8a00000, 0x00000000f8a00000, 0x00000000f8b00000| 0%| F| |TAMS 0x00000000f8a00000| PB 0x00000000f8a00000| Untracked +| 133|0x00000000f8b00000, 0x00000000f8b00000, 0x00000000f8c00000| 0%| F| |TAMS 0x00000000f8b00000| PB 0x00000000f8b00000| Untracked +| 134|0x00000000f8c00000, 0x00000000f8c00000, 0x00000000f8d00000| 0%| F| |TAMS 0x00000000f8c00000| PB 0x00000000f8c00000| Untracked +| 135|0x00000000f8d00000, 0x00000000f8d00000, 0x00000000f8e00000| 0%| F| |TAMS 0x00000000f8d00000| PB 0x00000000f8d00000| Untracked +| 136|0x00000000f8e00000, 0x00000000f8e00000, 0x00000000f8f00000| 0%| F| |TAMS 0x00000000f8e00000| PB 0x00000000f8e00000| Untracked +| 137|0x00000000f8f00000, 0x00000000f8f00000, 0x00000000f9000000| 0%| F| |TAMS 0x00000000f8f00000| PB 0x00000000f8f00000| Untracked +| 138|0x00000000f9000000, 0x00000000f9000000, 0x00000000f9100000| 0%| F| |TAMS 0x00000000f9000000| PB 0x00000000f9000000| Untracked +| 139|0x00000000f9100000, 0x00000000f9100000, 0x00000000f9200000| 0%| F| |TAMS 0x00000000f9100000| PB 0x00000000f9100000| Untracked +| 140|0x00000000f9200000, 0x00000000f9200000, 0x00000000f9300000| 0%| F| |TAMS 0x00000000f9200000| PB 0x00000000f9200000| Untracked +| 141|0x00000000f9300000, 0x00000000f9300000, 0x00000000f9400000| 0%| F| |TAMS 0x00000000f9300000| PB 0x00000000f9300000| Untracked +| 142|0x00000000f9400000, 0x00000000f9400000, 0x00000000f9500000| 0%| F| |TAMS 0x00000000f9400000| PB 0x00000000f9400000| Untracked +| 143|0x00000000f9500000, 0x00000000f9500000, 0x00000000f9600000| 0%| F| |TAMS 0x00000000f9500000| PB 0x00000000f9500000| Untracked +| 144|0x00000000f9600000, 0x00000000f9600000, 0x00000000f9700000| 0%| F| |TAMS 0x00000000f9600000| PB 0x00000000f9600000| Untracked +| 145|0x00000000f9700000, 0x00000000f9700000, 0x00000000f9800000| 0%| F| |TAMS 0x00000000f9700000| PB 0x00000000f9700000| Untracked +| 146|0x00000000f9800000, 0x00000000f9800000, 0x00000000f9900000| 0%| F| |TAMS 0x00000000f9800000| PB 0x00000000f9800000| Untracked +| 147|0x00000000f9900000, 0x00000000f9900000, 0x00000000f9a00000| 0%| F| |TAMS 0x00000000f9900000| PB 0x00000000f9900000| Untracked +| 148|0x00000000f9a00000, 0x00000000f9a00000, 0x00000000f9b00000| 0%| F| |TAMS 0x00000000f9a00000| PB 0x00000000f9a00000| Untracked +| 149|0x00000000f9b00000, 0x00000000f9b00000, 0x00000000f9c00000| 0%| F| |TAMS 0x00000000f9b00000| PB 0x00000000f9b00000| Untracked +| 150|0x00000000f9c00000, 0x00000000f9c00000, 0x00000000f9d00000| 0%| F| |TAMS 0x00000000f9c00000| PB 0x00000000f9c00000| Untracked +| 151|0x00000000f9d00000, 0x00000000f9d00000, 0x00000000f9e00000| 0%| F| |TAMS 0x00000000f9d00000| PB 0x00000000f9d00000| Untracked +| 152|0x00000000f9e00000, 0x00000000f9e00000, 0x00000000f9f00000| 0%| F| |TAMS 0x00000000f9e00000| PB 0x00000000f9e00000| Untracked +| 153|0x00000000f9f00000, 0x00000000f9f00000, 0x00000000fa000000| 0%| F| |TAMS 0x00000000f9f00000| PB 0x00000000f9f00000| Untracked +| 154|0x00000000fa000000, 0x00000000fa000000, 0x00000000fa100000| 0%| F| |TAMS 0x00000000fa000000| PB 0x00000000fa000000| Untracked +| 155|0x00000000fa100000, 0x00000000fa100000, 0x00000000fa200000| 0%| F| |TAMS 0x00000000fa100000| PB 0x00000000fa100000| Untracked +| 156|0x00000000fa200000, 0x00000000fa200000, 0x00000000fa300000| 0%| F| |TAMS 0x00000000fa200000| PB 0x00000000fa200000| Untracked +| 157|0x00000000fa300000, 0x00000000fa300000, 0x00000000fa400000| 0%| F| |TAMS 0x00000000fa300000| PB 0x00000000fa300000| Untracked +| 158|0x00000000fa400000, 0x00000000fa400000, 0x00000000fa500000| 0%| F| |TAMS 0x00000000fa400000| PB 0x00000000fa400000| Untracked +| 159|0x00000000fa500000, 0x00000000fa500000, 0x00000000fa600000| 0%| F| |TAMS 0x00000000fa500000| PB 0x00000000fa500000| Untracked +| 160|0x00000000fa600000, 0x00000000fa600000, 0x00000000fa700000| 0%| F| |TAMS 0x00000000fa600000| PB 0x00000000fa600000| Untracked +| 161|0x00000000fa700000, 0x00000000fa700000, 0x00000000fa800000| 0%| F| |TAMS 0x00000000fa700000| PB 0x00000000fa700000| Untracked +| 162|0x00000000fa800000, 0x00000000fa800000, 0x00000000fa900000| 0%| F| |TAMS 0x00000000fa800000| PB 0x00000000fa800000| Untracked +| 163|0x00000000fa900000, 0x00000000fa900000, 0x00000000faa00000| 0%| F| |TAMS 0x00000000fa900000| PB 0x00000000fa900000| Untracked +| 164|0x00000000faa00000, 0x00000000faa00000, 0x00000000fab00000| 0%| F| |TAMS 0x00000000faa00000| PB 0x00000000faa00000| Untracked +| 165|0x00000000fab00000, 0x00000000fab80800, 0x00000000fac00000| 50%| E| |TAMS 0x00000000fab00000| PB 0x00000000fab00000| Complete +| 166|0x00000000fac00000, 0x00000000fad00000, 0x00000000fad00000|100%| E|CS|TAMS 0x00000000fac00000| PB 0x00000000fac00000| Complete +| 167|0x00000000fad00000, 0x00000000fae00000, 0x00000000fae00000|100%| E|CS|TAMS 0x00000000fad00000| PB 0x00000000fad00000| Complete +| 168|0x00000000fae00000, 0x00000000faf00000, 0x00000000faf00000|100%| E|CS|TAMS 0x00000000fae00000| PB 0x00000000fae00000| Complete +| 169|0x00000000faf00000, 0x00000000fb000000, 0x00000000fb000000|100%| E|CS|TAMS 0x00000000faf00000| PB 0x00000000faf00000| Complete +| 170|0x00000000fb000000, 0x00000000fb100000, 0x00000000fb100000|100%| E|CS|TAMS 0x00000000fb000000| PB 0x00000000fb000000| Complete +| 171|0x00000000fb100000, 0x00000000fb200000, 0x00000000fb200000|100%| E|CS|TAMS 0x00000000fb100000| PB 0x00000000fb100000| Complete +| 172|0x00000000fb200000, 0x00000000fb300000, 0x00000000fb300000|100%| E|CS|TAMS 0x00000000fb200000| PB 0x00000000fb200000| Complete +| 173|0x00000000fb300000, 0x00000000fb400000, 0x00000000fb400000|100%| E|CS|TAMS 0x00000000fb300000| PB 0x00000000fb300000| Complete +| 174|0x00000000fb400000, 0x00000000fb500000, 0x00000000fb500000|100%| E|CS|TAMS 0x00000000fb400000| PB 0x00000000fb400000| Complete +| 175|0x00000000fb500000, 0x00000000fb600000, 0x00000000fb600000|100%| E|CS|TAMS 0x00000000fb500000| PB 0x00000000fb500000| Complete +| 176|0x00000000fb600000, 0x00000000fb700000, 0x00000000fb700000|100%| E|CS|TAMS 0x00000000fb600000| PB 0x00000000fb600000| Complete +| 177|0x00000000fb700000, 0x00000000fb800000, 0x00000000fb800000|100%| E|CS|TAMS 0x00000000fb700000| PB 0x00000000fb700000| Complete +| 178|0x00000000fb800000, 0x00000000fb900000, 0x00000000fb900000|100%| E|CS|TAMS 0x00000000fb800000| PB 0x00000000fb800000| Complete +| 179|0x00000000fb900000, 0x00000000fba00000, 0x00000000fba00000|100%| E|CS|TAMS 0x00000000fb900000| PB 0x00000000fb900000| Complete +| 180|0x00000000fba00000, 0x00000000fbb00000, 0x00000000fbb00000|100%| E|CS|TAMS 0x00000000fba00000| PB 0x00000000fba00000| Complete +| 181|0x00000000fbb00000, 0x00000000fbc00000, 0x00000000fbc00000|100%| E|CS|TAMS 0x00000000fbb00000| PB 0x00000000fbb00000| Complete +| 182|0x00000000fbc00000, 0x00000000fbd00000, 0x00000000fbd00000|100%| E|CS|TAMS 0x00000000fbc00000| PB 0x00000000fbc00000| Complete +| 183|0x00000000fbd00000, 0x00000000fbe00000, 0x00000000fbe00000|100%| E|CS|TAMS 0x00000000fbd00000| PB 0x00000000fbd00000| Complete +| 184|0x00000000fbe00000, 0x00000000fbf00000, 0x00000000fbf00000|100%| E|CS|TAMS 0x00000000fbe00000| PB 0x00000000fbe00000| Complete +| 185|0x00000000fbf00000, 0x00000000fc000000, 0x00000000fc000000|100%| E|CS|TAMS 0x00000000fbf00000| PB 0x00000000fbf00000| Complete +| 186|0x00000000fc000000, 0x00000000fc100000, 0x00000000fc100000|100%| E|CS|TAMS 0x00000000fc000000| PB 0x00000000fc000000| Complete +| 187|0x00000000fc100000, 0x00000000fc200000, 0x00000000fc200000|100%| E|CS|TAMS 0x00000000fc100000| PB 0x00000000fc100000| Complete +| 188|0x00000000fc200000, 0x00000000fc300000, 0x00000000fc300000|100%| E|CS|TAMS 0x00000000fc200000| PB 0x00000000fc200000| Complete +| 189|0x00000000fc300000, 0x00000000fc400000, 0x00000000fc400000|100%| E|CS|TAMS 0x00000000fc300000| PB 0x00000000fc300000| Complete +| 190|0x00000000fc400000, 0x00000000fc500000, 0x00000000fc500000|100%| E|CS|TAMS 0x00000000fc400000| PB 0x00000000fc400000| Complete +| 191|0x00000000fc500000, 0x00000000fc600000, 0x00000000fc600000|100%| E|CS|TAMS 0x00000000fc500000| PB 0x00000000fc500000| Complete +| 192|0x00000000fc600000, 0x00000000fc700000, 0x00000000fc700000|100%| E|CS|TAMS 0x00000000fc600000| PB 0x00000000fc600000| Complete +| 193|0x00000000fc700000, 0x00000000fc800000, 0x00000000fc800000|100%| E|CS|TAMS 0x00000000fc700000| PB 0x00000000fc700000| Complete +| 194|0x00000000fc800000, 0x00000000fc900000, 0x00000000fc900000|100%| E|CS|TAMS 0x00000000fc800000| PB 0x00000000fc800000| Complete +| 195|0x00000000fc900000, 0x00000000fca00000, 0x00000000fca00000|100%| E|CS|TAMS 0x00000000fc900000| PB 0x00000000fc900000| Complete +| 196|0x00000000fca00000, 0x00000000fcb00000, 0x00000000fcb00000|100%| E|CS|TAMS 0x00000000fca00000| PB 0x00000000fca00000| Complete +| 197|0x00000000fcb00000, 0x00000000fcc00000, 0x00000000fcc00000|100%| E|CS|TAMS 0x00000000fcb00000| PB 0x00000000fcb00000| Complete +| 198|0x00000000fcc00000, 0x00000000fcd00000, 0x00000000fcd00000|100%| E|CS|TAMS 0x00000000fcc00000| PB 0x00000000fcc00000| Complete +| 199|0x00000000fcd00000, 0x00000000fce00000, 0x00000000fce00000|100%| E|CS|TAMS 0x00000000fcd00000| PB 0x00000000fcd00000| Complete +| 200|0x00000000fce00000, 0x00000000fcf00000, 0x00000000fcf00000|100%| E|CS|TAMS 0x00000000fce00000| PB 0x00000000fce00000| Complete +| 201|0x00000000fcf00000, 0x00000000fd000000, 0x00000000fd000000|100%| E|CS|TAMS 0x00000000fcf00000| PB 0x00000000fcf00000| Complete +| 202|0x00000000fd000000, 0x00000000fd100000, 0x00000000fd100000|100%| E|CS|TAMS 0x00000000fd000000| PB 0x00000000fd000000| Complete +| 203|0x00000000fd100000, 0x00000000fd200000, 0x00000000fd200000|100%| E|CS|TAMS 0x00000000fd100000| PB 0x00000000fd100000| Complete +| 204|0x00000000fd200000, 0x00000000fd300000, 0x00000000fd300000|100%| S|CS|TAMS 0x00000000fd200000| PB 0x00000000fd200000| Complete +| 205|0x00000000fd300000, 0x00000000fd400000, 0x00000000fd400000|100%| S|CS|TAMS 0x00000000fd300000| PB 0x00000000fd300000| Complete +| 206|0x00000000fd400000, 0x00000000fd500000, 0x00000000fd500000|100%| S|CS|TAMS 0x00000000fd400000| PB 0x00000000fd400000| Complete +| 207|0x00000000fd500000, 0x00000000fd600000, 0x00000000fd600000|100%| S|CS|TAMS 0x00000000fd500000| PB 0x00000000fd500000| Complete +| 208|0x00000000fd600000, 0x00000000fd700000, 0x00000000fd700000|100%| S|CS|TAMS 0x00000000fd600000| PB 0x00000000fd600000| Complete +| 209|0x00000000fd700000, 0x00000000fd800000, 0x00000000fd800000|100%| E|CS|TAMS 0x00000000fd700000| PB 0x00000000fd700000| Complete +| 210|0x00000000fd800000, 0x00000000fd900000, 0x00000000fd900000|100%| E|CS|TAMS 0x00000000fd800000| PB 0x00000000fd800000| Complete +| 211|0x00000000fd900000, 0x00000000fda00000, 0x00000000fda00000|100%| E|CS|TAMS 0x00000000fd900000| PB 0x00000000fd900000| Complete +| 212|0x00000000fda00000, 0x00000000fdb00000, 0x00000000fdb00000|100%| E|CS|TAMS 0x00000000fda00000| PB 0x00000000fda00000| Complete +| 213|0x00000000fdb00000, 0x00000000fdc00000, 0x00000000fdc00000|100%| E|CS|TAMS 0x00000000fdb00000| PB 0x00000000fdb00000| Complete +| 214|0x00000000fdc00000, 0x00000000fdd00000, 0x00000000fdd00000|100%| E|CS|TAMS 0x00000000fdc00000| PB 0x00000000fdc00000| Complete +| 215|0x00000000fdd00000, 0x00000000fde00000, 0x00000000fde00000|100%| E|CS|TAMS 0x00000000fdd00000| PB 0x00000000fdd00000| Complete +| 216|0x00000000fde00000, 0x00000000fdf00000, 0x00000000fdf00000|100%| E|CS|TAMS 0x00000000fde00000| PB 0x00000000fde00000| Complete +| 217|0x00000000fdf00000, 0x00000000fe000000, 0x00000000fe000000|100%| E|CS|TAMS 0x00000000fdf00000| PB 0x00000000fdf00000| Complete +| 218|0x00000000fe000000, 0x00000000fe100000, 0x00000000fe100000|100%| E|CS|TAMS 0x00000000fe000000| PB 0x00000000fe000000| Complete +| 219|0x00000000fe100000, 0x00000000fe200000, 0x00000000fe200000|100%| E|CS|TAMS 0x00000000fe100000| PB 0x00000000fe100000| Complete +| 220|0x00000000fe200000, 0x00000000fe300000, 0x00000000fe300000|100%| E|CS|TAMS 0x00000000fe200000| PB 0x00000000fe200000| Complete +| 221|0x00000000fe300000, 0x00000000fe400000, 0x00000000fe400000|100%| E|CS|TAMS 0x00000000fe300000| PB 0x00000000fe300000| Complete +| 222|0x00000000fe400000, 0x00000000fe500000, 0x00000000fe500000|100%| E|CS|TAMS 0x00000000fe400000| PB 0x00000000fe400000| Complete +| 223|0x00000000fe500000, 0x00000000fe600000, 0x00000000fe600000|100%| E|CS|TAMS 0x00000000fe500000| PB 0x00000000fe500000| Complete +| 224|0x00000000fe600000, 0x00000000fe700000, 0x00000000fe700000|100%| E|CS|TAMS 0x00000000fe600000| PB 0x00000000fe600000| Complete +| 225|0x00000000fe700000, 0x00000000fe800000, 0x00000000fe800000|100%| E|CS|TAMS 0x00000000fe700000| PB 0x00000000fe700000| Complete +| 226|0x00000000fe800000, 0x00000000fe900000, 0x00000000fe900000|100%| E|CS|TAMS 0x00000000fe800000| PB 0x00000000fe800000| Complete +| 227|0x00000000fe900000, 0x00000000fea00000, 0x00000000fea00000|100%| E|CS|TAMS 0x00000000fe900000| PB 0x00000000fe900000| Complete +| 228|0x00000000fea00000, 0x00000000feb00000, 0x00000000feb00000|100%| E|CS|TAMS 0x00000000fea00000| PB 0x00000000fea00000| Complete +| 229|0x00000000feb00000, 0x00000000fec00000, 0x00000000fec00000|100%| E|CS|TAMS 0x00000000feb00000| PB 0x00000000feb00000| Complete +| 230|0x00000000fec00000, 0x00000000fed00000, 0x00000000fed00000|100%| E|CS|TAMS 0x00000000fec00000| PB 0x00000000fec00000| Complete +| 231|0x00000000fed00000, 0x00000000fee00000, 0x00000000fee00000|100%| E|CS|TAMS 0x00000000fed00000| PB 0x00000000fed00000| Complete +| 232|0x00000000fee00000, 0x00000000fef00000, 0x00000000fef00000|100%| E|CS|TAMS 0x00000000fee00000| PB 0x00000000fee00000| Complete +| 233|0x00000000fef00000, 0x00000000ff000000, 0x00000000ff000000|100%| E|CS|TAMS 0x00000000fef00000| PB 0x00000000fef00000| Complete +| 234|0x00000000ff000000, 0x00000000ff100000, 0x00000000ff100000|100%| E|CS|TAMS 0x00000000ff000000| PB 0x00000000ff000000| Complete +| 235|0x00000000ff100000, 0x00000000ff200000, 0x00000000ff200000|100%| E|CS|TAMS 0x00000000ff100000| PB 0x00000000ff100000| Complete +| 236|0x00000000ff200000, 0x00000000ff300000, 0x00000000ff300000|100%| E|CS|TAMS 0x00000000ff200000| PB 0x00000000ff200000| Complete +| 237|0x00000000ff300000, 0x00000000ff400000, 0x00000000ff400000|100%| E|CS|TAMS 0x00000000ff300000| PB 0x00000000ff300000| Complete +| 238|0x00000000ff400000, 0x00000000ff500000, 0x00000000ff500000|100%| E|CS|TAMS 0x00000000ff400000| PB 0x00000000ff400000| Complete +| 239|0x00000000ff500000, 0x00000000ff600000, 0x00000000ff600000|100%| E|CS|TAMS 0x00000000ff500000| PB 0x00000000ff500000| Complete +| 240|0x00000000ff600000, 0x00000000ff700000, 0x00000000ff700000|100%| E|CS|TAMS 0x00000000ff600000| PB 0x00000000ff600000| Complete +| 241|0x00000000ff700000, 0x00000000ff800000, 0x00000000ff800000|100%| E|CS|TAMS 0x00000000ff700000| PB 0x00000000ff700000| Complete +| 242|0x00000000ff800000, 0x00000000ff900000, 0x00000000ff900000|100%| E|CS|TAMS 0x00000000ff800000| PB 0x00000000ff800000| Complete +| 243|0x00000000ff900000, 0x00000000ffa00000, 0x00000000ffa00000|100%| E|CS|TAMS 0x00000000ff900000| PB 0x00000000ff900000| Complete +| 244|0x00000000ffa00000, 0x00000000ffb00000, 0x00000000ffb00000|100%| E|CS|TAMS 0x00000000ffa00000| PB 0x00000000ffa00000| Complete +| 245|0x00000000ffb00000, 0x00000000ffc00000, 0x00000000ffc00000|100%| E|CS|TAMS 0x00000000ffb00000| PB 0x00000000ffb00000| Complete +| 246|0x00000000ffc00000, 0x00000000ffd00000, 0x00000000ffd00000|100%| E|CS|TAMS 0x00000000ffc00000| PB 0x00000000ffc00000| Complete +| 247|0x00000000ffd00000, 0x00000000ffe00000, 0x00000000ffe00000|100%| E|CS|TAMS 0x00000000ffd00000| PB 0x00000000ffd00000| Complete +| 248|0x00000000ffe00000, 0x00000000ffe79000, 0x00000000fff00000| 47%|OA| |TAMS 0x00000000ffe00000| PB 0x00000000ffe00000| Untracked +| 249|0x00000000fff00000, 0x00000000fff83000, 0x0000000100000000| 51%|CA| |TAMS 0x00000000fff00000| PB 0x00000000fff00000| Untracked + +Card table byte_map: [0x00007ffff4a6f000,0x00007ffff4aec000] _byte_map_base: 0x00007ffff42ec000 + +Marking Bits: (CMBitMap*) 0x00007ffff0043560 + Bits: [0x00007ffff460a000, 0x00007ffff49f2000) + +Polling page: 0x00007ffff7ea3000 + +Metaspace: + +Usage: + Non-class: 6.61 MB used. + Class: 772.17 KB used. + Both: 7.36 MB used. + +Virtual space: + Non-class space: 64.00 MB reserved, 6.75 MB ( 11%) committed, 1 nodes. + Class space: 1.00 GB reserved, 896.00 KB ( <1%) committed, 1 nodes. + Both: 1.06 GB reserved, 7.62 MB ( <1%) committed. + +Chunk freelists: + Non-Class: 990.00 KB + Class: 3.09 MB + Both: 4.06 MB + +MaxMetaspaceSize: unlimited +CompressedClassSpaceSize: 1.00 GB +Initial GC threshold: 21.00 MB +Current GC threshold: 21.00 MB +CDS: on +MetaspaceReclaimPolicy: balanced + - commit_granule_bytes: 65536. + - commit_granule_words: 8192. + - virtual_space_node_default_size: 8388608. + - enlarge_chunks_in_place: 1. + - new_chunks_are_fully_committed: 0. + - uncommit_free_chunks: 1. + - use_allocation_guard: 0. + + +Internal statistics: + +num_allocs_failed_limit: 0. +num_arena_births: 142. +num_arena_deaths: 0. +num_vsnodes_births: 2. +num_vsnodes_deaths: 0. +num_space_committed: 122. +num_space_uncommitted: 0. +num_chunks_returned_to_freelist: 0. +num_chunks_taken_from_freelist: 215. +num_chunk_merges: 0. +num_chunk_splits: 120. +num_chunks_enlarged: 43. +num_inconsistent_stats: 0. + +CodeHeap 'non-profiled nmethods': size=120036Kb used=684Kb max_used=684Kb free=119351Kb + bounds [0x00007fffe087b000, 0x00007fffe0aeb000, 0x00007fffe7db4000] +CodeHeap 'profiled nmethods': size=120032Kb used=2030Kb max_used=2030Kb free=118001Kb + bounds [0x00007fffd8db4000, 0x00007fffd9024000, 0x00007fffe02ec000] +CodeHeap 'non-nmethods': size=5692Kb used=1697Kb max_used=1712Kb free=3994Kb + bounds [0x00007fffe02ec000, 0x00007fffe055c000, 0x00007fffe087b000] + total_blobs=1822 nmethods=1230 adapters=504 + compilation: enabled + stopped_count=0, restarted_count=0 + full_count=0 + +Compilation events (20 events): +Event: 3.246 Thread 0x00007ffff0162820 nmethod 1224 0x00007fffd8fa5610 code [0x00007fffd8fa5860, 0x00007fffd8fa6490] +Event: 3.247 Thread 0x00007ffff0162820 1217 3 java.lang.invoke.MethodType$ConcurrentWeakInternSet::get (47 bytes) +Event: 3.247 Thread 0x00007ffff0162820 nmethod 1217 0x00007fffd8fa6890 code [0x00007fffd8fa6aa0, 0x00007fffd8fa7278] +Event: 3.247 Thread 0x00007ffff0162820 1210 3 java.lang.invoke.LambdaForm$Name::replaceNames (175 bytes) +Event: 3.247 Thread 0x00007ffff0162820 nmethod 1210 0x00007fffd8fa7490 code [0x00007fffd8fa76c0, 0x00007fffd8fa82c0] +Event: 3.247 Thread 0x00007ffff0162820 1212 3 java.util.ImmutableCollections$List12::size (16 bytes) +Event: 3.248 Thread 0x00007ffff0162820 nmethod 1212 0x00007fffd8fa8610 code [0x00007fffd8fa87a0, 0x00007fffd8fa8930] +Event: 3.248 Thread 0x00007ffff0162820 1215 3 java.util.Arrays::copyOf (10 bytes) +Event: 3.248 Thread 0x00007ffff0162820 nmethod 1215 0x00007fffd8fa8990 code [0x00007fffd8fa8b20, 0x00007fffd8fa8c60] +Event: 3.248 Thread 0x00007ffff0162820 1211 3 jdk.internal.org.objectweb.asm.MethodWriter::visitAbstractType (8 bytes) +Event: 3.248 Thread 0x00007ffff0162820 nmethod 1211 0x00007fffd8fa8d10 code [0x00007fffd8fa8ea0, 0x00007fffd8fa8fd0] +Event: 3.248 Thread 0x00007ffff0162820 1225 3 java.lang.invoke.MethodType$ConcurrentWeakInternSet$WeakEntry:: (15 bytes) +Event: 3.248 Thread 0x00007ffff0161280 nmethod 1223 0x00007fffe0925c90 code [0x00007fffe0925e00, 0x00007fffe0926150] +Event: 3.248 Thread 0x00007ffff0162820 nmethod 1225 0x00007fffd8fa9090 code [0x00007fffd8fa9240, 0x00007fffd8fa9640] +Event: 3.265 Thread 0x00007ffff0162820 1228 3 java.util.Properties::loadConvert (540 bytes) +Event: 3.266 Thread 0x00007ffff0162820 nmethod 1228 0x00007fffd8fa9790 code [0x00007fffd8fa9a60, 0x00007fffd8faadc8] +Event: 3.267 Thread 0x00007ffff0162820 1229 % 3 java.util.Properties$LineReader::readLine @ 53 (584 bytes) +Event: 3.268 Thread 0x00007ffff0162820 nmethod 1229% 0x00007fffd8fab410 code [0x00007fffd8fab800, 0x00007fffd8fae7f0] +Event: 3.268 Thread 0x00007ffff0162820 1230 s 3 java.util.Properties::put (10 bytes) +Event: 3.269 Thread 0x00007ffff0162820 nmethod 1230 0x00007fffd8faf610 code [0x00007fffd8faf7c0, 0x00007fffd8fafa38] + +GC Heap History (18 events): +Event: 1.557 GC heap before +{Heap before GC invocations=0 (full 0): + garbage-first heap total 256000K, used 13296K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 12 young (12288K), 0 survivors (0K) + Metaspace used 2246K, committed 2432K, reserved 1114112K + class space used 233K, committed 320K, reserved 1048576K +} +Event: 1.562 GC heap after +{Heap after GC invocations=1 (full 0): + garbage-first heap total 256000K, used 5616K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 2 young (2048K), 2 survivors (2048K) + Metaspace used 2246K, committed 2432K, reserved 1114112K + class space used 233K, committed 320K, reserved 1048576K +} +Event: 1.651 GC heap before +{Heap before GC invocations=1 (full 0): + garbage-first heap total 256000K, used 15856K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 12 young (12288K), 2 survivors (2048K) + Metaspace used 2299K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.655 GC heap after +{Heap after GC invocations=2 (full 0): + garbage-first heap total 256000K, used 9176K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 2 young (2048K), 2 survivors (2048K) + Metaspace used 2299K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.705 GC heap before +{Heap before GC invocations=2 (full 0): + garbage-first heap total 256000K, used 19416K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 12 young (12288K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.708 GC heap after +{Heap after GC invocations=3 (full 0): + garbage-first heap total 256000K, used 12272K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 2 young (2048K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.749 GC heap before +{Heap before GC invocations=3 (full 0): + garbage-first heap total 256000K, used 22512K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 12 young (12288K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.751 GC heap after +{Heap after GC invocations=4 (full 0): + garbage-first heap total 256000K, used 14832K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 2 young (2048K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.803 GC heap before +{Heap before GC invocations=4 (full 0): + garbage-first heap total 256000K, used 26096K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 13 young (13312K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.805 GC heap after +{Heap after GC invocations=5 (full 0): + garbage-first heap total 256000K, used 17382K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 2 young (2048K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.913 GC heap before +{Heap before GC invocations=5 (full 0): + garbage-first heap total 256000K, used 36838K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 21 young (21504K), 2 survivors (2048K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 1.918 GC heap after +{Heap after GC invocations=6 (full 0): + garbage-first heap total 256000K, used 20944K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 3 young (3072K), 3 survivors (3072K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.004 GC heap before +{Heap before GC invocations=6 (full 0): + garbage-first heap total 256000K, used 42448K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 24 young (24576K), 3 survivors (3072K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.010 GC heap after +{Heap after GC invocations=7 (full 0): + garbage-first heap total 256000K, used 24560K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 3 young (3072K), 3 survivors (3072K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.104 GC heap before +{Heap before GC invocations=7 (full 0): + garbage-first heap total 256000K, used 48112K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 26 young (26624K), 3 survivors (3072K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.109 GC heap after +{Heap after GC invocations=8 (full 0): + garbage-first heap total 256000K, used 28656K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 4 young (4096K), 4 survivors (4096K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.230 GC heap before +{Heap before GC invocations=8 (full 0): + garbage-first heap total 256000K, used 64496K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 39 young (39936K), 4 survivors (4096K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} +Event: 2.236 GC heap after +{Heap after GC invocations=9 (full 0): + garbage-first heap total 256000K, used 33776K [0x00000000f0600000, 0x0000000100000000) + region size 1024K, 5 young (5120K), 5 survivors (5120K) + Metaspace used 2301K, committed 2432K, reserved 1114112K + class space used 236K, committed 320K, reserved 1048576K +} + +Dll operation events (10 events): +Event: 0.164 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjava.so +Event: 0.498 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjsvml.so +Event: 0.620 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libverify.so +Event: 0.763 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libnio.so +Event: 0.775 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjimage.so +Event: 0.844 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libzip.so +Event: 0.941 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libawt.so +Event: 0.945 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libawt_headless.so +Event: 1.519 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libnet.so +Event: 3.136 Loaded shared library /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libfontmanager.so + +Deoptimization events (20 events): +Event: 3.203 Thread 0x00007fff3c000e60 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007fffe08cdbc4 relative=0x0000000000000124 +Event: 3.203 Thread 0x00007fff3c000e60 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007fffe08cdbc4 method=java.nio.charset.CharsetDecoder.decode(Ljava/nio/ByteBuffer;Ljava/nio/CharBuffer;Z)Ljava/nio/charset/CoderResult; @ 15 c2 +Event: 3.203 Thread 0x00007fff3c000e60 DEOPT PACKING pc=0x00007fffe08cdbc4 sp=0x00007fffc9e05980 +Event: 3.203 Thread 0x00007fff3c000e60 DEOPT UNPACKING pc=0x00007fffe0308799 sp=0x00007fffc9e05928 mode 2 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: trap_request=0xffffffde fr.pc=0x00007fffe08e78e0 relative=0x00000000000001c0 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00007fffe08e78e0 method=java.nio.Buffer.(IIIILjava/lang/foreign/MemorySegment;)V @ 39 c2 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT PACKING pc=0x00007fffe08e78e0 sp=0x00007fffc9e05370 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT UNPACKING pc=0x00007fffe0308799 sp=0x00007fffc9e05348 mode 2 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: trap_request=0xffffffc6 fr.pc=0x00007fffe08f6638 relative=0x0000000000000b18 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: reason=bimorphic_or_optimized_type_check action=maybe_recompile pc=0x00007fffe08f6638 method=java.util.regex.Pattern$Start.match(Ljava/util/regex/Matcher;ILjava/lang/CharSequence;)Z @ 44 c2 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT PACKING pc=0x00007fffe08f6638 sp=0x00007fffc9e05bb0 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT UNPACKING pc=0x00007fffe0308799 sp=0x00007fffc9e05b20 mode 2 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: trap_request=0xffffff45 fr.pc=0x00007fffe08f6560 relative=0x0000000000000a40 +Event: 3.205 Thread 0x00007fff3c000e60 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00007fffe08f6560 method=java.util.regex.Matcher.search(I)Z @ 76 c2 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT PACKING pc=0x00007fffe08f6560 sp=0x00007fffc9e05b40 +Event: 3.205 Thread 0x00007fff3c000e60 DEOPT UNPACKING pc=0x00007fffe0308799 sp=0x00007fffc9e05b40 mode 2 +Event: 3.222 Thread 0x00007fff3c000e60 Uncommon trap: trap_request=0xffffffde fr.pc=0x00007fffe08e78e0 relative=0x00000000000001c0 +Event: 3.222 Thread 0x00007fff3c000e60 Uncommon trap: reason=class_check action=maybe_recompile pc=0x00007fffe08e78e0 method=java.nio.Buffer.(IIIILjava/lang/foreign/MemorySegment;)V @ 39 c2 +Event: 3.222 Thread 0x00007fff3c000e60 DEOPT PACKING pc=0x00007fffe08e78e0 sp=0x00007fffc9e058d0 +Event: 3.222 Thread 0x00007fff3c000e60 DEOPT UNPACKING pc=0x00007fffe0308799 sp=0x00007fffc9e058a8 mode 2 + +Classes loaded (20 events): +Event: 3.225 Loading class java/net/spi/InetAddressResolverProvider +Event: 3.226 Loading class java/net/spi/InetAddressResolverProvider done +Event: 3.227 Loading class java/net/Inet6Address +Event: 3.227 Loading class java/net/Inet6Address done +Event: 3.227 Loading class java/net/Inet6Address$Inet6AddressHolder +Event: 3.228 Loading class java/net/Inet6Address$Inet6AddressHolder done +Event: 3.229 Loading class sun/net/InetAddressCachePolicy +Event: 3.238 Loading class sun/net/InetAddressCachePolicy done +Event: 3.238 Loading class sun/net/InetAddressCachePolicy$1 +Event: 3.239 Loading class sun/net/InetAddressCachePolicy$1 done +Event: 3.239 Loading class sun/net/InetAddressCachePolicy$2 +Event: 3.239 Loading class sun/net/InetAddressCachePolicy$2 done +Event: 3.239 Loading class java/net/InetAddress$CachedAddresses +Event: 3.240 Loading class java/net/InetAddress$CachedAddresses done +Event: 3.240 Loading class java/net/InetAddress$CachedLocalHost +Event: 3.240 Loading class java/net/InetAddress$CachedLocalHost done +Event: 3.296 Loading class sun/font/FontConfigManager$FcCompFont +Event: 3.296 Loading class sun/font/FontConfigManager$FcCompFont done +Event: 3.296 Loading class sun/font/FontConfigManager$FontConfigFont +Event: 3.296 Loading class sun/font/FontConfigManager$FontConfigFont done + +Classes unloaded (0 events): +No events + +Classes redefined (0 events): +No events + +Internal exceptions (10 events): +Event: 0.896 Thread 0x00007ffff00195d0 Exception (0x00000000ffdf0080) +thrown [src/hotspot/share/classfile/systemDictionary.cpp, line 305] +Event: 0.958 Thread 0x00007ffff00195d0 Exception (0x00000000ffc544f8) +thrown [src/hotspot/share/prims/jni.cpp, line 519] +Event: 0.967 Thread 0x00007ffff00195d0 Exception (0x00000000ffc7e5b0) +thrown [src/hotspot/share/prims/jni.cpp, line 519] +Event: 2.431 Thread 0x00007fff3c000e60 Implicit null exception at 0x00007fffe08b8bdf to 0x00007fffe08bb214 +Event: 2.445 Thread 0x00007fff3c000e60 Implicit null exception at 0x00007fffe08c9c76 to 0x00007fffe08c9f80 +Event: 2.464 Thread 0x00007fff3c000e60 Exception (0x00000000fb71fc20) +thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 772] +Event: 2.882 Thread 0x00007fff3c000e60 Exception (0x00000000fad4c928) +thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 772] +Event: 2.928 Thread 0x00007fff3c000e60 Exception (0x00000000fad76e88) +thrown [src/hotspot/share/interpreter/linkResolver.cpp, line 772] +Event: 3.021 Thread 0x00007fff3c000e60 Exception (0x00000000fac655e8) +thrown [src/hotspot/share/classfile/systemDictionary.cpp, line 305] +Event: 3.023 Thread 0x00007fff3c000e60 Exception (0x00000000fac69578) +thrown [src/hotspot/share/classfile/systemDictionary.cpp, line 305] + +VM Operations (20 events): +Event: 1.705 Executing VM operation: G1CollectForAllocation +Event: 1.708 Executing VM operation: G1CollectForAllocation done +Event: 1.749 Executing VM operation: G1CollectForAllocation +Event: 1.751 Executing VM operation: G1CollectForAllocation done +Event: 1.803 Executing VM operation: G1CollectForAllocation +Event: 1.805 Executing VM operation: G1CollectForAllocation done +Event: 1.913 Executing VM operation: G1CollectForAllocation +Event: 1.918 Executing VM operation: G1CollectForAllocation done +Event: 2.004 Executing VM operation: G1CollectForAllocation +Event: 2.010 Executing VM operation: G1CollectForAllocation done +Event: 2.104 Executing VM operation: G1CollectForAllocation +Event: 2.109 Executing VM operation: G1CollectForAllocation done +Event: 2.230 Executing VM operation: G1CollectForAllocation +Event: 2.236 Executing VM operation: G1CollectForAllocation done +Event: 2.453 Executing VM operation: HandshakeAllThreads +Event: 2.453 Executing VM operation: HandshakeAllThreads done +Event: 2.565 Executing VM operation: HandshakeAllThreads +Event: 2.565 Executing VM operation: HandshakeAllThreads done +Event: 3.223 Executing VM operation: HandshakeAllThreads +Event: 3.223 Executing VM operation: HandshakeAllThreads done + +Events (20 events): +Event: 0.533 Thread 0x00007ffff015cf50 Thread added: 0x00007ffff015cf50 +Event: 0.533 Protecting memory [0x00007fffd875b000,0x00007fffd875f000] with protection modes 0 +Event: 0.533 Thread 0x00007ffff015e3e0 Thread added: 0x00007ffff015e3e0 +Event: 0.533 Protecting memory [0x00007fffd865a000,0x00007fffd865e000] with protection modes 0 +Event: 0.533 Thread 0x00007ffff015f860 Thread added: 0x00007ffff015f860 +Event: 0.533 Protecting memory [0x00007fffd8559000,0x00007fffd855d000] with protection modes 0 +Event: 0.533 Thread 0x00007ffff0161280 Thread added: 0x00007ffff0161280 +Event: 0.533 Protecting memory [0x00007fffd8458000,0x00007fffd845c000] with protection modes 0 +Event: 0.533 Thread 0x00007ffff0162820 Thread added: 0x00007ffff0162820 +Event: 0.533 Protecting memory [0x00007fffd8357000,0x00007fffd835b000] with protection modes 0 +Event: 0.548 Thread 0x00007ffff01791d0 Thread added: 0x00007ffff01791d0 +Event: 0.548 Protecting memory [0x00007fffd8256000,0x00007fffd825a000] with protection modes 0 +Event: 0.578 Thread 0x00007ffff017d980 Thread added: 0x00007ffff017d980 +Event: 0.578 Protecting memory [0x00007fffd8053000,0x00007fffd8057000] with protection modes 0 +Event: 1.386 Thread 0x00007ffff0242360 Thread added: 0x00007ffff0242360 +Event: 1.386 Protecting memory [0x00007fffc9e08000,0x00007fffc9e0c000] with protection modes 0 +Event: 1.386 Thread 0x00007fff3c000e60 Thread added: 0x00007fff3c000e60 +Event: 1.386 Protecting memory [0x00007fffc9d07000,0x00007fffc9d0b000] with protection modes 0 +Event: 2.573 Thread 0x00007fff300f0d80 Thread added: 0x00007fff300f0d80 +Event: 2.576 Protecting memory [0x00007fffc9c06000,0x00007fffc9c0a000] with protection modes 0 + + +Dynamic libraries: +f0600000-ffe00000 rw-p 00000000 00:00 0 +ffe00000-ffe79000 rw-p 00d2f000 00:59 5629611 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/server/classes.jsa +ffe79000-fff00000 rw-p 00000000 00:00 0 +fff00000-fff83000 rw-p 00cac000 00:59 5629611 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/server/classes.jsa +fff83000-100000000 rw-p 00000000 00:00 0 +555555554000-555555555000 r--p 00000000 00:59 22859802 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/bin/java +555555555000-555555556000 r-xp 00001000 00:59 22859802 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/bin/java 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/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjli.so +7ffff7ff8000-7ffff7ff9000 r--p 0000e000 00:59 14202370 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjli.so +7ffff7ff9000-7ffff7ffa000 rw-p 0000f000 00:59 14202370 /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm/lib/libjli.so +7ffff7ffa000-7ffff7ffc000 rw-p 00000000 00:00 0 +7ffff7ffc000-7ffff7ffd000 r--p 0002e000 103:03 33556263 /usr/lib64/ld-2.28.so +7ffff7ffd000-7ffff7fff000 rw-p 0002f000 103:03 33556263 /usr/lib64/ld-2.28.so +7ffffffdc000-7ffffffff000 rw-p 00000000 00:00 0 [stack] +8000000d5000-8000000d9000 r--p 00000000 00:00 0 [vvar] +8000000d9000-8000000db000 r-xp 00000000 00:00 0 [vdso] +ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] + + +VM Arguments: +jvm_args: -Xms250m -Xmx250m -Dfastqc.output_dir=/scratch/jobs/46158308/tmpff74icft -Dfastqc.threads=1 -Dfastqc.quiet=true -XX:ParallelGCThreads=1 -Djava.awt.headless=true +java_command: uk.ac.babraham.FastQC.FastQCApplication /scratch/tweber/DATA/MC_DATA/STOCKS/2024-01-30-AACT75KM5/HGSVCpool3NEWp2/fastq/HGSVCpool3NEWp2iTRUE11A33.2.fastq.gz +java_class_path (initial): /g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/sam-1.103.jar:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/jbzip2-0.9.jar:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/cisd-jhdf5.jar +Launcher Type: SUN_STANDARD + +[Global flags] + intx CICompilerCount = 2 {product} {ergonomic} + uint ConcGCThreads = 1 {product} {ergonomic} + uint G1ConcRefinementThreads = 1 {product} {ergonomic} + size_t G1HeapRegionSize = 1048576 {product} {ergonomic} + uintx GCDrainStackTargetSize = 64 {product} {ergonomic} + size_t InitialHeapSize = 262144000 {product} {command line} + size_t MarkStackSize = 4194304 {product} {ergonomic} + size_t MaxHeapSize = 262144000 {product} {command line} + size_t MaxNewSize = 157286400 {product} {ergonomic} + size_t MinHeapDeltaBytes = 1048576 {product} {ergonomic} + size_t MinHeapSize = 262144000 {product} {command line} + uintx NonNMethodCodeHeapSize = 5826188 {pd product} {ergonomic} + uintx NonProfiledCodeHeapSize = 122916026 {pd product} {ergonomic} + uint ParallelGCThreads = 1 {product} {command line} + uintx ProfiledCodeHeapSize = 122916026 {pd product} {ergonomic} + uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic} + bool SegmentedCodeCache = true {product} {ergonomic} + size_t SoftMaxHeapSize = 262144000 {manageable} {ergonomic} + bool UseCompressedClassPointers = true {product lp64_product} {ergonomic} + bool UseCompressedOops = true {product lp64_product} {ergonomic} + bool UseG1GC = true {product} {ergonomic} + +Logging: +Log output configuration: + #0: stdout all=warning uptime,level,tags foldmultilines=false + #1: stderr all=off uptime,level,tags foldmultilines=false + +Environment Variables: +JAVA_HOME=/g/korbel2/weber/workspace/mosaicatcher-update/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/lib/jvm +CLASSPATH=/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/sam-1.103.jar:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/jbzip2-0.9.jar:/g/korbel2/weber/workspace/mosaicatcher-update/workflow/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/opt/fastqc-0.11.9/cisd-jhdf5.jar +PATH=/g/korbel2/weber/workspace/mosaicatcher-update/.snakemake/conda/aad828ebb249cffe2fd94f222ca0cee1_/bin:/biolo/ngs/bin:/biolo/ngs/bin:/g/korbel2/weber/miniconda3/envs/snakemake_panoptesfix/bin:/g/korbel2/weber/miniconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin +SHELL=/bin/bash +LANG=en_US.UTF-8 +LC_ALL=en_US.UTF-8 +LC_CTYPE=C +TERM=xterm-256color +TMPDIR=/scratch/jobs/46158308 +TMP=/scratch/jobs/46158308 +TEMP=/scratch/jobs/46158308 + +Active Locale: +LC_ALL=en_US.UTF-8 +LC_COLLATE=en_US.UTF-8 +LC_CTYPE=en_US.UTF-8 +LC_MESSAGES=en_US.UTF-8 +LC_MONETARY=en_US.UTF-8 +LC_NUMERIC=en_US.UTF-8 +LC_TIME=en_US.UTF-8 + +Signal Handlers: + SIGSEGV: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked + SIGBUS: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked + SIGFPE: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked + SIGPIPE: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGXFSZ: javaSignalHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGILL: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked + SIGUSR2: SR_handler in libjvm.so, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked + SIGHUP: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGINT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGTERM: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGQUIT: UserHandler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, blocked + SIGTRAP: crash_handler in libjvm.so, mask=11100100010111111101111111111110, flags=SA_RESTART|SA_SIGINFO, unblocked + + +--------------- S Y S T E M --------------- + +OS: +Rocky Linux release 8.9 (Green Obsidian) +uname: Linux 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Wed Nov 29 18:55:19 UTC 2023 x86_64 +OS uptime: 1 days 4:29 hours +libc: glibc 2.28 NPTL 2.28 +rlimit (soft/hard): STACK 8192k/infinity , CORE 0k/infinity , NPROC 1544329/1544329 , NOFILE 131072/131072 , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK 64k/infinity +load average: 350.75 302.42 289.82 + +/proc/meminfo: +MemTotal: 395387924 kB +MemFree: 234914488 kB +MemAvailable: 280088512 kB +Buffers: 7308 kB +Cached: 47933480 kB +SwapCached: 10432 kB +Active: 6345788 kB +Inactive: 147763376 kB +Active(anon): 119732 kB +Inactive(anon): 106077064 kB +Active(file): 6226056 kB +Inactive(file): 41686312 kB +Unevictable: 245904 kB +Mlocked: 245904 kB +SwapTotal: 131068 kB +SwapFree: 77364 kB +Dirty: 236 kB +Writeback: 116 kB +AnonPages: 106380380 kB +Mapped: 35243368 kB +Shmem: 4220 kB +KReclaimable: 715528 kB +Slab: 2310376 kB +SReclaimable: 715528 kB +SUnreclaim: 1594848 kB +KernelStack: 64112 kB +PageTables: 539632 kB +NFS_Unstable: 0 kB +Bounce: 0 kB +WritebackTmp: 0 kB +CommitLimit: 197825028 kB +Committed_AS: 101422844 kB +VmallocTotal: 13743895347199 kB +VmallocUsed: 384416 kB +VmallocChunk: 0 kB +Percpu: 669696 kB +HardwareCorrupted: 0 kB +AnonHugePages: 19738624 kB +ShmemHugePages: 0 kB +ShmemPmdMapped: 0 kB +FileHugePages: 0 kB +FilePmdMapped: 0 kB +HugePages_Total: 0 +HugePages_Free: 0 +HugePages_Rsvd: 0 +HugePages_Surp: 0 +Hugepagesize: 2048 kB +Hugetlb: 0 kB +DirectMap4k: 645820 kB +DirectMap2M: 44199936 kB +DirectMap1G: 358612992 kB + +/sys/kernel/mm/transparent_hugepage/enabled: [always] madvise never +/sys/kernel/mm/transparent_hugepage/defrag (defrag/compaction efforts parameter): always defer defer+madvise [madvise] never + +Process Memory: +Virtual Size: 3414536K (peak: 3414536K) +Resident Set Size: 185832K (peak: 185832K) (anon: 160832K, file: 25000K, shmem: 0K) +Swapped out: 0K +C-Heap outstanding allocations: 18281K, retained: 6038K +glibc malloc tunables: (default) + +/proc/sys/kernel/threads-max (system-wide limit on the number of threads): 3088659 +/proc/sys/vm/max_map_count (maximum number of memory map areas a process may have): 65530 +/proc/sys/kernel/pid_max (system-wide limit on number of process identifiers): 4194304 + +container (cgroup) information: +container_type: cgroupv1 +cpu_cpuset_cpus: 126,254 +cpu_memory_nodes: 0-15 +active_processor_count: 2 +cpu_quota: no quota +cpu_period: 100000 +cpu_shares: no shares +memory_limit_in_bytes: 2252800 k +memory_and_swap_limit_in_bytes: 2252800 k +memory_soft_limit_in_bytes: unlimited +memory_usage_in_bytes: 363280 k +memory_max_usage_in_bytes: 363280 k +kernel_memory_usage_in_bytes: 29588 k +kernel_memory_max_usage_in_bytes: unlimited +kernel_memory_limit_in_bytes: 29592 k +maximum number of tasks: unlimited +current number of tasks: 1260 + +Steal ticks since vm start: 0 +Steal ticks percentage since vm start: 0.000 + +CPU: total 256 (initial active 2) (256 cores per cpu, 2 threads per core) family 25 model 160 stepping 2 microcode 0xaa00205, cx8, cmov, fxsr, ht, mmx, 3dnowpref, sse, sse2, sse3, ssse3, sse4a, sse4.1, sse4.2, popcnt, lzcnt, tsc, tscinvbit, avx, avx2, aes, erms, clmul, bmi1, bmi2, adx, avx512f, avx512dq, avx512cd, avx512bw, avx512vl, sha, fma, vzeroupper, avx512_vpopcntdq, avx512_vpclmulqdq, avx512_vaes, avx512_vnni, clflush, clflushopt, avx512_vbmi2, avx512_vbmi, rdtscp, rdpid, fsrm, gfni, avx512_bitalg, f16c, pku, ospke, cet_ss, avx512_ifma +CPU Model and flags from /proc/cpuinfo: +model name : AMD EPYC 9754 128-Core Processor +flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good amd_lbr_v2 nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba perfmon_v2 ibrs ibpb stibp ibrs_enhanced vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local avx512_bf16 clzero irperf xsaveerptr wbnoinvd amd_ppin cppc arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif x2avic v_spec_ctrl avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq la57 rdpid overflow_recov succor smca fsrm flush_l1d + +Online cpus: 0-255 +Offline cpus: +BIOS frequency limitation: 2250000 +Frequency switch latency (ns): 0 +Available cpu frequencies: 2250000 1800000 1500000 +Current governor: userspace +Core performance/turbo boost: 1 + +Memory: 4k page, physical 2252800k(1889304k free), swap 131068k(77364k free) +Page Sizes: 4k + +vm_info: OpenJDK 64-Bit Server VM (20.0.2-internal-adhoc..src) for linux-amd64 JRE (20.0.2-internal-adhoc..src), built on 2023-09-09T00:58:05Z by "" with gcc 12.3.0 + +END. diff --git a/watchdog_pipeline/excluded_samples.yaml b/watchdog_pipeline/excluded_samples.yaml index e119dec9..96b41cc5 100644 --- a/watchdog_pipeline/excluded_samples.yaml +++ b/watchdog_pipeline/excluded_samples.yaml @@ -1,15 +1,20 @@ excluded_samples: - - "PDAC60590" # MICE - - "PDAC60590MNI" # MICE - - "DXR30hMaja" # MICE - - "DXR42hMaja" # MICE - - "GM19705" # ERROR to investigate - - "OrgxDoxocx02" # ERROR Multistep - - "GM20355x01" # ERROR Multistep - - "10uMDXR42hx01" # ERROR Multistep - - "mESCx01" # ERROR Multistep - - "DXR100nMxS2x01" # ERROR Multistep - - "MRD48hx02" # ERROR Multistep - - "RPEx03" # ERROR Only 48 cells + - "GM19705" # ERROR to investigate + - "OrgxDoxocx02" # ERROR Multistep + - "GM20355x01" # ERROR Multistep + - "10uMDXR42hx01" # ERROR Multistep + - "mESCx01" # ERROR Multistep + - "DXR100nMxS2x01" # ERROR Multistep + - "MRD48hx02" # ERROR Multistep + - "RPEx03" # ERROR Only 48 cells # OLD - - "ckAML02x02" # ashleys_library_size_normalisation + - "ckAML02x02" # ashleys_library_size_normalisation + +tagged_samples: + mm10: + - "PDAC60590" # MICE + - "PDAC60590MNI" # MICE + - "DXR30hMaja" # MICE + - "DXR42hMaja" # MICE + - "LanexLorenzoNPCAPH24hnewSortUVLED" + - "LanexLorenzoNPCDMSO18holdSortUVLED" diff --git a/watchdog_pipeline/watchdog_pipeline.py b/watchdog_pipeline/watchdog_pipeline.py index c7024563..d42d92d7 100644 --- a/watchdog_pipeline/watchdog_pipeline.py +++ b/watchdog_pipeline/watchdog_pipeline.py @@ -1,9 +1,8 @@ import sqlite3 import time import os, sys, glob, subprocess, re +import numpy as np import requests -from watchdog.observers import Observer -from watchdog.events import FileSystemEventHandler from datetime import datetime import logging import json @@ -14,6 +13,7 @@ from pathlib import Path import pika import yaml # RabbitMQ +import hashlib os.makedirs("watchdog/logs", exist_ok=True) @@ -34,9 +34,9 @@ # main_path_to_watch = sys.argv[1] paths_to_watch = [ - "/g/korbel/shared/data/others/StrandSeq/runs", + # "/g/korbel/shared/data/others/StrandSeq/runs", # "/g/korbel/shared/genecore", - # "/g/korbel/STOCKS/Data/Assay/sequencing", + "/g/korbel/STOCKS/Data/Assay/sequencing", ] dry_run = sys.argv[1] @@ -48,18 +48,12 @@ # publishdir_location = "/g/korbel/weber/TMP/WORKFLOW_RESULTS_DEV" publishdir_location = "/g/korbel/WORKFLOW_RESULTS" # genecore_prefix = paths_to_watch[0] + profile_slurm = [ "--profile", "/g/korbel2/weber/workspace/snakemake_profiles/HPC/dev/slurm_legacy_conda/", ] -# profile_slurm = [ -# "--profile", -# "/g/korbel2/weber/workspace/snakemake_profiles/local/conda_singularity/", -# "--cores", -# "64", -# "--singularity-args", -# '"-B /scratch,/g"', -# ] + # profile_slurm = [ # "--profile", # "/g/korbel2/weber/workspace/mosaicatcher-update/workflow/snakemake_profiles/HPC/dev/slurm_EMBL/", @@ -72,10 +66,13 @@ "1", ] dry_run_options = ["-n", "-q"] + # snakemake_binary = "/g/korbel2/weber/miniconda3/envs/snakemake_latest/bin/snakemake" + snakemake_binary = ( "/g/korbel2/weber/miniconda3/envs/snakemake_panoptesfix/bin/snakemake" ) + # Panoptes pipeline = sys.argv[4] print(pipeline) @@ -83,7 +80,6 @@ "ashleys-qc-pipeline", "mosaicatcher-pipeline", ], "Pipeline not correct" -# pipeline = "ashleys-qc-pipeline" my_env = os.environ.copy() snakemake_binary_folder = "/".join(snakemake_binary.split("/")[:-1]) @@ -118,9 +114,7 @@ def generate_data_file(directory): if plate.split("-")[0][:2] == "20": for sample in os.listdir(os.path.join(directory, plate)): if "sample" not in unwanted: - counts_stats_file_path = os.path.join( - directory, plate, sample, "counts", f"{sample}.info_raw" - ) + counts_stats_file_path = os.path.join() labels_file_path = os.path.join( directory, plate, sample, "cell_selection", "labels.tsv" ) @@ -150,1031 +144,981 @@ def generate_data_file(directory): # TODO: push df to parquet & reuse the same for ashleys stats -# Define the event handler -class MyHandler(FileSystemEventHandler): - def on_created(self, event): - if event.is_directory: # if a directory is created - logging.info(f"Directory {event.src_path} has been created!") - self.process_new_directory(event.src_path) - - def extract_samples_names(self, l, directory_path): - samples = list() - prefixes = list() - plate_types = list() - - pattern = re.compile(r"_lane1(.*?)(iTRU|PE20)(.*?)([A-H]?)(\d{2})(?:_1_|_2_)") - - # First pass: Count occurrences of each sample_name - file_counts_per_sample = Counter() - for file_path in l: - match = pattern.search(file_path) - if match: - sample_name = match.group(1) - file_counts_per_sample[sample_name] += 1 - - # print(directory_path) - # print(file_counts_per_sample) - - # Second pass: Process files and determine plate type per sample - for j, file_path in enumerate(sorted(l)): - match = pattern.search(file_path) - if match: - sample_name = match.group(1) - - file_count = file_counts_per_sample[sample_name] - - # Determine plate type using modulo 96 operation - # if file_count % 96 != 0: - # # raise ValueError( - # print( - # f"Invalid file count for sample {sample_name} with file count {file_count}. Must be a multiple of 96." - # ) - # continue - plate_type = int(file_count / 2) - - if (j + 1) % file_count == 0: - if not sample_name or len(sample_name) == 0: - continue - prefixes.append(match.group(2)) - plate = directory_path.split("/")[-1] - samples.append(sample_name) - plate_types.append(plate_type) - - return prefixes, samples, plate_types - - def check_date(self, plate): - from datetime import datetime, timedelta - - date_str = "-".join(plate.split("-")[:-1]) - date_format = "%Y-%m-%d" - folder_date = datetime.strptime(date_str, date_format) - - # Calculate the date that is 6 months before today - six_months_ago = datetime.now() - timedelta( - days=3 * 30 - ) # This assumes an average of 30 days in a month - # print(plate, six_months_ago, folder_date > six_months_ago) - # Compare dates - return folder_date > six_months_ago - - @staticmethod - def load_from_json(filename: str): - """Load the data from the JSON file.""" - try: - with open(filename, "r") as file: - data = json.load(file) - return data - except (FileNotFoundError, json.JSONDecodeError): - # If the file does not exist or there's an error in reading it, - # return an empty dictionary or other default value - return {} - - @staticmethod - def update_timestamps(directory): - """ - Update the access and modification times of all files in the given directory and its subdirectories. - - :param directory: Path to the directory - """ - for root, dirs, files in os.walk(directory): - for file in files: - if file.endswith(".fastq.gz"): - continue - try: - file_path = Path(root) / file - current_time = time.time() - os.utime(file_path, (current_time, current_time)) - logging.info(f"Updated timestamp for: {file_path}") - except FileNotFoundError: - logging.info(f"File not found: {file_path}") - - # Example usage - # directory_path = "/path/to/your/directory" - # update_timestamps(directory_path) - - def consume_last_message_from_rabbitmq(self, json_backup_filename=str, queue=str): - pika_connection = pika.BlockingConnection( - pika.ConnectionParameters(host="localhost") - ) - channel = pika_connection.channel() +def extract_samples_names(l, directory_path): + samples = list() + prefixes = list() + plate_types = list() - # Fetch the message without auto acknowledgment - method_frame, header_frame, body = channel.basic_get( - queue=queue, auto_ack=False - ) + pattern = re.compile(r"_lane1(.*?)(iTRU|PE20)(.*?)([A-H]?)(\d{2})(?:_1_|_2_)") - if method_frame: - # Extract the timestamp from the header frame - # if header_frame.timestamp: - timestamp = header_frame.timestamp - human_readable_timestamp = datetime.fromtimestamp( - timestamp / 1000.0 - ).strftime("%Y-%m-%d %H:%M:%S") + # First pass: Count occurrences of each sample_name + file_counts_per_sample = Counter() + for file_path in l: + match = pattern.search(file_path) + if match: + sample_name = match.group(1) + file_counts_per_sample[sample_name] += 1 - # else: - # timestamp = None - # Convert timestamp to human-readable format if necessary - - # # Acknowledge the message after processing - channel.basic_nack(delivery_tag=method_frame.delivery_tag, requeue=True) - # pika_connection.close() - data = json.loads(body.decode("utf-8")) - print(data) - # if data dict is empty - if not data: - print("EXITING") - sys.exit("RabbitMQ queue NOT empty but message is") - # print("Loading from JSON file...") - # data_json = self.load_from_json(filename=json_backup_filename) - # file_timestamp = os.path.getmtime(json_backup_filename) - # file_timestamp = datetime.fromtimestamp(file_timestamp).strftime( - # "%Y-%m-%d %H:%M:%S" - # ) - # return data_json, file_timestamp - else: - print("RabbitMQ queue NOT empty and message is NOT empty") - print(data) - return data, human_readable_timestamp + # print(directory_path) + # print(file_counts_per_sample) - else: - if os.path.exists(json_backup_filename): - pika_connection.close() - print("No message available, RabbitMQ queue is empty") - print("Loading from JSON file...") - data_json = self.load_from_json(filename=json_backup_filename) - file_timestamp = os.path.getmtime(json_backup_filename) - file_timestamp = datetime.fromtimestamp(file_timestamp).strftime( - "%Y-%m-%d %H:%M:%S" - ) + # Second pass: Process files and determine plate type per sample + for j, file_path in enumerate(sorted(l)): + match = pattern.search(file_path) + if match: + sample_name = match.group(1) - return data_json, file_timestamp - else: - current_time = datetime.now().strftime("%Y-%m-%d %H:%M:%S") - return {"workflows": []}, current_time - - # Function to get all workflows - @staticmethod - def get_workflows(): - url = "http://localhost:8058/api/workflows" - response = requests.get(url) - if response.status_code == 200: - return response.json() - else: - raise Exception( - "Failed to fetch data: Status code {}".format(response.status_code) - ) + file_count = file_counts_per_sample[sample_name] - # Function to find a workflow ID by name - @staticmethod - def find_workflow_id_by_name(workflows, name): - for workflow in workflows.get("workflows", []): - if workflow["name"] == name: - return workflow - return None - - # Function to load YAML configuration - @staticmethod - def load_config(file_path): - with open(file_path, "r") as file: - return yaml.safe_load(file) - - # Function to process each sample - def process_sample( - self, - sample_name, - plate, - pipeline, - data_location, - publishdir_location, - variable, - workflows_data, - last_message_timestamp, - prefixes, - plate_type, - path_to_watch, - ): - run_id = f"{pipeline}--{plate}--{sample_name}" - workflow_id = self.find_workflow_id_by_name(workflows_data, run_id) - - dict_variables = { - f"{variable}_scratch": False, - f"{variable}_scratch_ts": False, - f"{variable}_scratch_rdays": None, - f"{variable}_report": False, - } - - # ashleys_final_scratch = False - # ashleys_report = False - # ashleys_final_scratch_timestamp = None - # ashleys_rdays = None - - # mosaicatcher_final_scratch = False - # mosaicatcher_report = False - # mosaicatcher_final_scratch_timestamp = None - # mc_rdays = None - - if os.path.isfile( - f"{publishdir_location}/{plate}/{sample_name}/reports/{sample_name}_{pipeline}_report.zip" - ): - # report = True - dict_variables[f"{variable}_report"] = True - - if pipeline == "ashleys-qc-pipeline": - if os.path.isfile( - f"{data_location}/{plate}/{sample_name}/config/ashleys_final_results.ok" - # f"{data_location}/{plate}/{sample_name}/multiqc/multiqc_report/multiqc_report.html" - ): - # ashleys_final_scratch = True - ts = os.path.getmtime( - f"{data_location}/{plate}/{sample_name}/config/ashleys_final_results.ok" + # Determine plate type using modulo 96 operation + if file_count % 96 != 0: + # raise ValueError( + print( + f"Invalid file count for sample {sample_name} with file count {file_count}. Must be a multiple of 96." ) - ts = datetime.fromtimestamp(ts) - dict_variables[f"{variable}_scratch"] = True - dict_variables[f"{variable}_scratch_ts"] = ts - - # to datetime and then strfmtime - - # computing remaning days to reach 5 months between ashleys_final_scratch_timestamp and now - rdays = (datetime.now() - ts).days - rdays = 150 - rdays - - dict_variables[f"{variable}_scratch_rdays"] = rdays - elif pipeline == "mosaicatcher-pipeline": - if os.path.isfile( - f"{data_location}/{plate}/{sample_name}/plots/final_results/{sample_name}.txt" - # f"{data_location}/{plate}/{sample_name}/multiqc/multiqc_report/multiqc_report.html" - ): - ts = os.path.getmtime( - f"{data_location}/{plate}/{sample_name}/plots/final_results/{sample_name}.txt" - ) - ts = datetime.fromtimestamp(ts) - dict_variables[f"{variable}_scratch"] = True - dict_variables[f"{variable}_scratch_ts"] = ts - # to datetime and then strfmtime - # computing remaning days to reach 5 months between ashleys_final_scratch_timestamp and now - rdays = (datetime.now() - ts).days - rdays = 150 - rdays - - dict_variables[f"{variable}_scratch_rdays"] = rdays - - if not workflow_id: - workflow_id = { - "id": "None", - "status": "None", - "started_at": last_message_timestamp, - "completed_at": last_message_timestamp, - "jobs_done": "None", - "jobs_total": "None", - } - else: - workflow_id["started_at"] = datetime.strptime( - workflow_id["started_at"], - "%a, %d %b %Y %H:%M:%S GMT", - ).strftime("%Y-%m-%d %H:%M:%S.%f") - - if workflow_id["completed_at"] is not None: - workflow_id["completed_at"] = datetime.strptime( - workflow_id["completed_at"], - "%a, %d %b %Y %H:%M:%S GMT", - ).strftime("%Y-%m-%d %H:%M:%S.%f") - - year = plate.split("-")[0] - run_path = ( - f"{path_to_watch}/{year}/{plate}" - if year in ["2023", "2024"] - else f"{path_to_watch}/{plate}" - ) + continue + plate_type = int(file_count / 2) - # turn the print into a dict - tmp_d = { - "panoptes_id": workflow_id["id"], - "plate": plate, - "sample": sample_name, - # "report": report, - # "labels": labels, - # "ashleys_final_scratch": ashleys_final_scratch, - # "ashleys_final_scratch_timestamp": ashleys_final_scratch_timestamp, - # "ashleys_rdays": ashleys_rdays, - # "mosaicatcher_final_scratch": mosaicatcher_final_scratch, - # "mosaicatcher_final_scratch_timestamp": mosaicatcher_final_scratch_timestamp, - # "mc_rdays": mc_rdays, - "report": dict_variables[f"{variable}_report"], - # "ashleys_final_scratch": ashleys_final_scratch, - # "ashleys_final_scratch_timestamp": ashleys_final_scratch_timestamp, - # "ashleys_rdays": ashleys_rdays, - "final_output_scratch": dict_variables[f"{variable}_scratch"], - "scratch_ts": dict_variables[f"{variable}_scratch_ts"], - "scratch_rdays": dict_variables[f"{variable}_scratch_rdays"], - "status": workflow_id["status"], - "prefix": list(prefixes)[0], - "plate_type": plate_type, - "started_at": workflow_id["started_at"], - "completed_at": workflow_id["completed_at"], - "jobs_done": workflow_id["jobs_done"], - "jobs_total": workflow_id["jobs_total"], - "run_path": run_path, - } - print(tmp_d) - return tmp_d - - # Main function to process directories - def process_directories( - self, - paths_to_watch, - excluded_samples, - pipeline, - data_location, - publishdir_location, - variable, - workflows_data, - last_message_timestamp, + if (j + 1) % file_count == 0: + if not sample_name or len(sample_name) == 0: + continue + prefixes.append(match.group(2)) + plate = directory_path.split("/")[-1] + samples.append(sample_name) + plate_types.append(plate_type) + # Compute the hash at the folder level + hash = hashlib.sha256() + # List all files in the directory and sort them + files = glob.glob(f"{directory_path}/*") + files.sort() + # Loop over the sorted list of files and update the hash + for file in files: + # Get file attributes: name, modification timestamp, and size + stats = os.stat(file) + file_info = f"{os.path.basename(file)}-{stats.st_mtime}-{stats.st_size}" + + hash.update(file_info.encode("utf-8")) + + # Get the final hash value in hexadecimal format + folder_hash = hash.hexdigest() + + return prefixes, samples, plate_types, folder_hash + + +def check_date(plate): + from datetime import datetime, timedelta + + date_str = "-".join(plate.split("-")[:-1]) + date_format = "%Y-%m-%d" + folder_date = datetime.strptime(date_str, date_format) + + # Calculate the date that is 6 months before today + six_months_ago = datetime.now() - timedelta( + days=3 * 30 + ) # This assumes an average of 30 days in a month + # print(plate, six_months_ago, folder_date > six_months_ago) + # Compare dates + return folder_date > six_months_ago + + +def load_from_json(filename: str): + """Load the data from the JSON file.""" + try: + with open(filename, "r") as file: + data = json.load(file) + return data + except (FileNotFoundError, json.JSONDecodeError): + # If the file does not exist or there's an error in reading it, + # return an empty dictionary or other default value + return {} + + +def update_timestamps(directory): + """ + Update the access and modification times of all files in the given directory and its subdirectories. + + :param directory: Path to the directory + """ + for root, dirs, files in os.walk(directory): + for file in files: + if file.endswith(".fastq.gz"): + continue + try: + file_path = Path(root) / file + current_time = time.time() + os.utime(file_path, (current_time, current_time)) + logging.info(f"Updated timestamp for: {file_path}") + except FileNotFoundError: + logging.info(f"File not found: {file_path}") + + +def load_config(file_path): + with open(file_path, "r") as file: + return yaml.safe_load(file) + + +# Function to process each sample +def process_sample( + sample_name, + plate, + pipeline, + data_location, + publishdir_location, + variable, + prefixes, + plate_type, + path_to_watch, + folder_hash, + config, +): + dict_variables = { + f"{variable}_scratch": False, + f"{variable}_scratch_ts": False, + f"{variable}_scratch_rdays": None, + # f"aqc_report": False, + f"mc_report": False, + "mm10": False, + } + + if sample_name in config["tagged_samples"]["mm10"]: + dict_variables["mm10"] = True + + if os.path.isfile( + f"{publishdir_location}/{plate}/{sample_name}/reports/{sample_name}_{pipeline}_report.zip" ): - unwanted = ["._.DS_Store", ".DS_Store", "config"] - - main_df = [] - if len(workflows_data) > 0: - for path_to_watch in paths_to_watch: - total_list_runs = [] - - if path_to_watch == "/g/korbel/STOCKS/Data/Assay/sequencing": - for year in os.listdir(path_to_watch): - if year.startswith( - "20" - ): # Assuming directories starting with "20" are years - year_path = os.path.join(path_to_watch, year) - for folder in os.listdir(year_path): - folder_path = os.path.join(year_path, folder) - if ( - os.path.isdir(folder_path) - and folder not in unwanted - ): - total_list_runs.append(folder_path) - else: - total_list_runs = [ - os.path.join(path_to_watch, e) - for e in os.listdir(path_to_watch) - if e not in unwanted - and os.path.isdir(os.path.join(path_to_watch, e)) - ] - - print(total_list_runs) - - for directory_path in total_list_runs: - print(directory_path) - prefixes, samples, plate_types = self.extract_samples_names( - glob.glob(f"{directory_path}/*.txt.gz"), - directory_path, - ) - - if len(set(prefixes)) == 1: - for sample_name, plate_type in zip(samples, plate_types): - if sample_name not in excluded_samples: - os.makedirs( - f"{publishdir_location}/{os.path.basename(directory_path)}/{sample_name}/reports", - exist_ok=True, - ) - result = self.process_sample( - sample_name, - os.path.basename(directory_path), - pipeline, - data_location, - publishdir_location, - variable, - workflows_data, - last_message_timestamp, - prefixes, - plate_type, - path_to_watch, - ) - main_df.append(result) - return pd.DataFrame(main_df) - - def check_unprocessed_folder(self): - connection = sqlite3.connect( - "/g/korbel2/weber/workspace/strandscape/.panoptes.db" - ) + # report = True + variable = "aqc" if pipeline == "ashleys-qc-pipeline" else "mc" - # # Get the list of processed plates from rabbitmq - message = self.consume_last_message_from_rabbitmq( - json_backup_filename="watchdog/processing_status.json", - queue="data_panoptes", - ) + dict_variables[f"{variable}_report"] = True + + info_file = f"{data_location}/{plate}/{sample_name}/counts/{sample_name}.info" + nb_usable_cells = None + snp_file = f"{data_location}/{plate}/{sample_name}/snv_calls/check_SNVs_nb.txt" + check_snp = None + + if os.path.isfile(info_file): + nb_usable_cells = pd.read_csv(info_file, sep="\t", skiprows=13).shape[0] + ts = os.path.getmtime(info_file) + ts = datetime.fromtimestamp(ts) + dict_variables[f"{variable}_scratch_ts"] = ts + # to datetime and then strfmtime + # computing remaning days to reach 5 months between ashleys_final_scratch_timestamp and now + rdays = (datetime.now() - ts).days + rdays = 150 - rdays + dict_variables[f"{variable}_scratch_rdays"] = rdays + + if os.path.isfile(snp_file): + nb_snps = pd.read_csv(snp_file, sep="\t") + check_snp = nb_snps.loc[nb_snps["SNP_nb"] > 100].shape[0] == nb_snps.shape[0] + + if os.path.isfile( + f"{data_location}/{plate}/{sample_name}/plots/final_results/{sample_name}.txt" + # f"{data_location}/{plate}/{sample_name}/multiqc/multiqc_report/multiqc_report.html" + ): + dict_variables[f"{variable}_scratch"] = True - # list_runs_processed = sorted( - # [e for e in os.listdir(data_location) if e not in unwanted] - # ) + year = plate.split("-")[0] + run_path = ( + f"{path_to_watch}/{year}/{plate}" + if year in ["2023", "2024"] + else f"{path_to_watch}/{plate}" + ) - # unprocessed_plates = sorted(list(set(total_list_runs).difference(list_runs_processed))) - unprocessed_plates = list() - # workflows_data = self.get_workflows() - workflows_data = message[0] - last_message_timestamp = message[1] - print(last_message_timestamp) - last_message_timestamp = datetime.strptime( - last_message_timestamp, "%Y-%m-%d %H:%M:%S" - ).strftime("%Y-%m-%d %H:%M:%S.%f") + # Compute status + status = None + if ( + dict_variables[f"mc_report"] is True + and dict_variables[f"{variable}_scratch"] is True + ): + status = "Completed" + elif ( + dict_variables[f"mc_report"] is True + and dict_variables[f"{variable}_scratch"] is False + and nb_usable_cells is None + ): + status = "Error" + # elif ( + # dict_variables[f"mc_report"] is False + # and dict_variables[f"{variable}_scratch"] is False + # # and nb_usable_cells is not None + # # and nb_usable_cells > 5 + # ): + # status = "To process" + elif ( + dict_variables[f"mc_report"] is True + and dict_variables[f"{variable}_scratch"] is False + and nb_usable_cells is not None + and nb_usable_cells <= 5 + ): + status = "Too low nb of cells" + elif dict_variables[f"mc_report"] is False and ( + dict_variables[f"{variable}_scratch"] is True + ): + status = "MC Report missing" + elif dict_variables[f"mc_report"] is False and (nb_usable_cells is not None): + status = "AQC Report missing" + + elif plate_type % 96 != 0: + status = "Non canonical plate" + + else: + status = "To process" + + if dict_variables["mm10"] is True: + status = "mm10 sample" + + # turn the print into a dict + tmp_d = { + "plate": plate, + "sample": sample_name, + "report_mc": dict_variables[f"mc_report"], + "final_output_scratch": dict_variables[f"{variable}_scratch"], + "nb_usable_cells": nb_usable_cells, + "check_snp": check_snp, + "scratch_ts": dict_variables[f"{variable}_scratch_ts"], + "scratch_rdays": dict_variables[f"{variable}_scratch_rdays"], + "prefix": list(prefixes)[0], + "plate_type": plate_type, + "folder_hash": folder_hash, + "run_path": run_path, + "mm10": dict_variables["mm10"], + "status": status, + } + return tmp_d + + +# Main function to process directories +def process_directories( + paths_to_watch, + config, + pipeline, + data_location, + publishdir_location, + variable, + ref_df, +): + unwanted = ["._.DS_Store", ".DS_Store", "config"] - # last_message_timestamp = last_message_timestamp + if ref_df.empty is False: + ref_df_plates = ref_df["plate"].unique().tolist() + else: + ref_df_plates = [] + + main_df = [] + total_list_runs = [] + + # if len(workflows_data) > 0: + for path_to_watch in paths_to_watch: + if path_to_watch == "/g/korbel/STOCKS/Data/Assay/sequencing": + for year in os.listdir(path_to_watch): + print(year) + if year.startswith( + "20" + ): # Assuming directories starting with "20" are years + year_path = os.path.join(path_to_watch, year) + for folder in os.listdir(year_path): + # if folder.startswith("2024-01-22-H2F3YAFX7"): + folder_path = os.path.join(year_path, folder) + if os.path.isdir(folder_path) and folder not in unwanted: + total_list_runs.append(folder_path) + else: + for e in os.listdir(path_to_watch): + if e not in unwanted and os.path.isdir(os.path.join(path_to_watch, e)): + total_list_runs.append(os.path.join(path_to_watch, e)) - variable = "aqc" if pipeline == "ashleys-qc-pipeline" else "mc" + # exclude plates from the ref_df in the total_list_runs + print(total_list_runs) + print("EXCLUDE") - # Get the list of excluded samples from the config - config = self.load_config("watchdog_pipeline/excluded_samples.yaml") - # TODO: add run in the excluded list - excluded_samples = config["excluded_samples"] + # total_list_runs = sorted(list(set(total_list_runs).difference(set(ref_df_plates)))) + # print(total_list_runs) - main_df = self.process_directories( - paths_to_watch, - excluded_samples, - pipeline, - data_location, - publishdir_location, - variable, - workflows_data, - last_message_timestamp, + for directory_path in total_list_runs: + print(directory_path) + prefixes, samples, plate_types, folder_hash = extract_samples_names( + glob.glob(f"{directory_path}/*.txt.gz"), + directory_path, ) - pd.options.display.max_rows = 999 - pd.options.display.max_colwidth = 70 - - main_df = pd.DataFrame(main_df) - # print(main_df) - # exit() - # main_df.loc[(main_df["labels"] == True) & (main_df["report"] == True), "real_status"] = "Completed" - main_df.loc[ - (main_df["final_output_scratch"] == True) & (main_df["report"] == False), - "real_status", - ] = "Report missing" - main_df.loc[ - (main_df["final_output_scratch"] == False) & (main_df["report"] == True), - "real_status", - ] = "Error" - main_df.loc[ - (main_df["final_output_scratch"] == False) & (main_df["report"] == False), - "real_status", - ] = "To process" - main_df.loc[ - (main_df["final_output_scratch"] == True) - & (main_df["report"] == True) - & (main_df["status"] == "None"), - "real_status", - ] = "Error" - main_df.loc[ - (main_df["final_output_scratch"] == True) - & (main_df["report"] == True) - & (main_df["status"] == "Running"), - "real_status", - ] = "Running" - main_df.loc[ - (main_df["final_output_scratch"] == True) - & (main_df["report"] == True) - & (main_df["status"] == "Done"), - "real_status", - ] = "Completed" - main_df["real_status"] = main_df["real_status"].fillna( - "Error (to investigate))" - ) - print(workflows_data["workflows"]) - - print("\n") - logging.info(f"Pipeline selected {pipeline}") - print("\n") - - print(main_df) - print(main_df.run_path.values[0]) - test_json = main_df.to_json(orient="records", date_format="iso") - # print(test_json) - # print(pd.read_json(test_json, orient="records")) - # exit() - - # pipeline_final_file_variable = ( - # "ashleys_final_scratch" - # if pipeline == "ashleys_qc_pipeline" - # else "mosaicatcher_final_scratch" - # ) + if len(set(prefixes)) == 1: + for sample_name, plate_type in zip(samples, plate_types): + # if sample_name not in config["excluded_samples"]: + os.makedirs( + f"{publishdir_location}/{os.path.basename(directory_path)}/{sample_name}/reports", + exist_ok=True, + ) + result = process_sample( + sample_name, + os.path.basename(directory_path), + pipeline, + data_location, + publishdir_location, + variable, + prefixes, + plate_type, + path_to_watch, + folder_hash, + config, + ) + main_df.append(result) + return pd.DataFrame(main_df) - dry_run_db = False - if dry_run_db is False: - cursor = connection.cursor() +def check_unprocessed_folder(): + ref_df_path = "watchdog/processing_status.tsv" - # assert ( - # main_df.loc[ - # (main_df["final_output_scratch"] == False) - # & (main_df["report"] == True) - # ].shape[0] - # == 0 - # ), "Error in table, samples have report done without the completion of the pipeline" + if os.path.isfile(ref_df_path): + ref_df = pd.read_csv(ref_df_path, sep="\t") + print("Ref df") + # get timestamp + ref_df_ts = os.path.getmtime(ref_df_path) + ref_df_ts = datetime.fromtimestamp(ref_df_ts) + print(ref_df_ts) + print(ref_df) - # logging.info( - # "Correcting status of plates with report.zip and final_output_scratch" - # ) + else: + ref_df = pd.DataFrame() + print("No ref df") - # for row in main_df.loc[ - # (main_df["final_output_scratch"] == True) - # & (main_df["report"] == True) - # & (main_df["status"] != "Done") - # ].to_dict("records"): - # logging.info(row) - # panoptes_entry = f"{pipeline}--{row['plate']}--{row['sample']}" - # workflow_id = row["panoptes_id"] - - # # if workflow_id != "None": - # # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' - # # subprocess.run(command, shell=True, check=True) - - # panoptes_data = [ - # e for e in workflows_data["workflows"] if e["id"] == workflow_id - # ] - - # print(panoptes_entry) - # print(panoptes_data) - # print(row) - # if workflow_id and workflow_id != "None": - # assert ( - # len(panoptes_data) > 0 - # ), f"Data issue between pika & panoptes, {str(panoptes_data)}" - - # if panoptes_data: - # panoptes_data = panoptes_data[0] - # if "completed_at" not in panoptes_data: - # panoptes_data["completed_at"] = last_message_timestamp - - # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' - # subprocess.run(command, shell=True, check=True) - - # else: - # logging.info("Panoptes data not found for workflow entry: %s", row) - # panoptes_data = { - # "started_at": last_message_timestamp, - # "completed_at": last_message_timestamp, - # "jobs_done": "1", - # "jobs_total": "1", - # } - - # print(row) - - # cursor.execute( - # """ - # INSERT INTO workflows (name, status, done, total, started_at, completed_at) - # VALUES (?, ?, ?, ?, ?, ?) - # """, - # ( - # panoptes_entry, - # "Done", - # panoptes_data["jobs_done"], - # panoptes_data["jobs_total"], - # panoptes_data["started_at"], - # panoptes_data["completed_at"], - # ), - # ) - # connection.commit() - - logging.info( - "Processing plates without final_output_scratch or outdated without report.zip" - ) + # Get the list of excluded samples from the config + config = load_config("watchdog_pipeline/excluded_samples.yaml") + # TODO: add run in the excluded list - for row in main_df.loc[ - (main_df["final_output_scratch"] == False) - # & (main_df["report"] == False) - ].to_dict("records"): - # panoptes = True if row["status"] == "None" else False - # panoptes = True - if row["plate"].split("-")[0][:2] == "20": - # if row["plate"].split("-")[0] == "2024": - logging.info(row) - - if dry_run == "False": - if row["panoptes_id"] != "None": - workflow_id = row["panoptes_id"] - panoptes_data = [ - e - for e in workflows_data["workflows"] - if e["id"] == workflow_id - ] - command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' - subprocess.run(command, shell=True, check=True) - - self.process_new_directory( - row["run_path"], - # "/".join([path_to_watch, row["plate"]]), - row["prefix"], - row["sample"], - row["plate_type"], - report_only=False, - panoptes=panoptes, - ) - - # logging.info( - # "Processing plates not present anymore on scratch and without report.zip" - # ) + variable = "aqc" if pipeline == "ashleys-qc-pipeline" else "mc" - # for row in main_df.loc[ - # # (main_df["multiqc_scratch"] == False) - # (main_df["final_output_scratch"] == False) - # # & (main_df["report"] == False) - # ].to_dict("records"): - # logging.info(row) - - # # panoptes = True if row["status"] == "None" else False - # # panoptes = True - - # if dry_run == "False": - # if row["panoptes_id"] != "None": - # workflow_id = row["panoptes_id"] - # panoptes_data = [ - # e - # for e in workflows_data["workflows"] - # if e["id"] == workflow_id - # ] - # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' - # subprocess.run(command, shell=True, check=True) - - # self.process_new_directory( - # "/".join([path_to_watch, row["plate"]]), - # row["prefix"], - # row["sample"], - # row["plate_type"], - # report_only=False, - # panoptes=panoptes, - # ) - - logging.info( - "Processing plates without report.zip but with labels.tsv and still on scratch" - ) + main_df = process_directories( + paths_to_watch, + config, + pipeline, + data_location, + publishdir_location, + variable, + ref_df, + ) - for row in main_df.loc[ - (main_df["final_output_scratch"] == True) - & (main_df["scratch_rdays"] > 2) - & (main_df["report"] == False) - ].to_dict("records"): - logging.info(row) + pd.options.display.max_rows = 999 + pd.options.display.max_colwidth = 70 + print(main_df) + + if ref_df.empty is False: + # Compare hash for each plate and sample that has status "To process" between the ref_df and the main_df + main_df_to_process = ( + main_df.loc[main_df["status"] == "To process", ["plate", "folder_hash"]] + .drop_duplicates() + .set_index("plate") + .to_dict("index") + ) + print(main_df_to_process) + ref_df_to_process = ( + ref_df.loc[ + ref_df["plate"].isin(list(main_df_to_process.keys())), + ["plate", "folder_hash"], + ] + .drop_duplicates() + .set_index("plate") + .to_dict("index") + ) + for plate, folder_hash in main_df_to_process.items(): + if plate in ref_df_to_process: + print( + plate, + folder_hash["folder_hash"], + ref_df_to_process[plate]["folder_hash"], + ) + if ( + folder_hash["folder_hash"] + != ref_df_to_process[plate]["folder_hash"] + ): + main_df.loc[ + main_df["plate"] == plate, "status" + ] = "Copy not complete" + # else: + # main_df.loc[main_df["plate"] == plate, "status"] = "To process (2)" + + print(main_df) + + main_df.to_csv(ref_df_path, sep="\t", index=False) + + # print(main_df) + # exit() + # main_df.loc[(main_df["labels"] == True) & (main_df["report"] == True), "real_status"] = "Completed" + # main_df.loc[ + # (main_df["final_output_scratch"] == True) & (main_df["report_mc"] == False), + # "real_status", + # ] = "MC Report missing" + # main_df.loc[ + # (main_df["final_output_scratch"] == False) & (main_df["report_mc"] == True), + # "real_status", + # ] = "Error" + # main_df.loc[ + # (main_df["final_output_scratch"] == False) + # & (main_df["report_mc"] == False), + # "real_status", + # ] = "To process" + # main_df.loc[ + # (main_df["final_output_scratch"] == True) + # & (main_df["report_mc"] == True) + # & (main_df["status"] == "None"), + # "real_status", + # ] = "Error" + # main_df.loc[ + # (main_df["final_output_scratch"] == True) + # & (main_df["report_mc"] == True) + # & (main_df["status"] == "Running"), + # "real_status", + # ] = "Running" + # main_df.loc[ + # (main_df["final_output_scratch"] == True) + # & (main_df["report_mc"] == True) + # & (main_df["status"] == "Done"), + # "real_status", + # ] = "Completed" + # main_df["real_status"] = main_df["real_status"].fillna( + # "Error (to investigate))" + # ) + # print(workflows_data["workflows"]) + + # print("\n") + # logging.info(f"Pipeline selected {pipeline}") + # print("\n") + + # print(main_df) + # print(main_df.run_path.values[0]) + # test_json = main_df.to_json(orient="records", date_format="iso") + # print(test_json) + # print(pd.read_json(test_json, orient="records")) + # exit() + + # pipeline_final_file_variable = ( + # "ashleys_final_scratch" + # if pipeline == "ashleys_qc_pipeline" + # else "mosaicatcher_final_scratch" + # ) + + dry_run_db = False + + if dry_run_db is False: + # cursor = connection.cursor() + + # assert ( + # main_df.loc[ + # (main_df["final_output_scratch"] == False) + # & (main_df["report"] == True) + # ].shape[0] + # == 0 + # ), "Error in table, samples have report done without the completion of the pipeline" + + # logging.info( + # "Correcting status of plates with report.zip and final_output_scratch" + # ) - # panoptes = True if row["status"] == "None" else False - # panoptes = False - panoptes_entry = f"{pipeline}--{row['plate']}--{row['sample']}" + # for row in main_df.loc[ + # (main_df["final_output_scratch"] == True) + # & (main_df["report"] == True) + # & (main_df["status"] != "Done") + # ].to_dict("records"): + # logging.info(row) + # panoptes_entry = f"{pipeline}--{row['plate']}--{row['sample']}" + # workflow_id = row["panoptes_id"] + + # # if workflow_id != "None": + # # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' + # # subprocess.run(command, shell=True, check=True) + + # panoptes_data = [ + # e for e in workflows_data["workflows"] if e["id"] == workflow_id + # ] + + # print(panoptes_entry) + # print(panoptes_data) + # print(row) + # if workflow_id and workflow_id != "None": + # assert ( + # len(panoptes_data) > 0 + # ), f"Data issue between pika & panoptes, {str(panoptes_data)}" + + # if panoptes_data: + # panoptes_data = panoptes_data[0] + # if "completed_at" not in panoptes_data: + # panoptes_data["completed_at"] = last_message_timestamp + + # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' + # subprocess.run(command, shell=True, check=True) + + # else: + # logging.info("Panoptes data not found for workflow entry: %s", row) + # panoptes_data = { + # "started_at": last_message_timestamp, + # "completed_at": last_message_timestamp, + # "jobs_done": "1", + # "jobs_total": "1", + # } + + # print(row) + + # cursor.execute( + # """ + # INSERT INTO workflows (name, status, done, total, started_at, completed_at) + # VALUES (?, ?, ?, ?, ?, ?) + # """, + # ( + # panoptes_entry, + # "Done", + # panoptes_data["jobs_done"], + # panoptes_data["jobs_total"], + # panoptes_data["started_at"], + # panoptes_data["completed_at"], + # ), + # ) + # connection.commit() + + logging.info( + "Processing plates without final_output_scratch or outdated without report.zip" + ) + + for row in main_df.loc[ + (main_df["status"] == "To process") + # & (main_df["report"] == False) + ].to_dict("records"): + # panoptes = True if row["status"] == "None" else False + # panoptes = True + # if row["plate_type"] % 96 == 0: + # if pd.isna(row["nb_usable_cells"]) or row["nb_usable_cells"] > 5: + if row["plate"].split("-")[0][:2] == "20": + # if row["plate"].split("-")[0] == "2024": + logging.info(row) if dry_run == "False": - self.process_new_directory( - "/".join([path_to_watch, row["plate"]]), + # if row["panoptes_id"] != "None": + # workflow_id = row["panoptes_id"] + # panoptes_data = [ + # e + # for e in workflows_data["workflows"] + # if e["id"] == workflow_id + # ] + # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' + # subprocess.run(command, shell=True, check=True) + + process_new_directory( + row["run_path"], + # "/".join([path_to_watch, row["plate"]]), row["prefix"], row["sample"], row["plate_type"], - report_only=True, + report_only=False, panoptes=panoptes, ) - if row["panoptes_id"] != "None": - workflow_id = row["panoptes_id"] - panoptes_data = [ - e - for e in workflows_data["workflows"] - if e["id"] == workflow_id - ][0] - - if panoptes_data: - command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' - subprocess.run(command, shell=True, check=True) - - cursor.execute( - """ - INSERT INTO workflows (name, status, done, total, started_at, completed_at) - VALUES (?, ?, ?, ?, ?, ?) - """, - ( - panoptes_entry, - "Done", - panoptes_data["jobs_done"], - panoptes_data["jobs_total"], - panoptes_data["started_at"], - panoptes_data["completed_at"], - ), - ) - connection.commit() + # logging.info( + # "Processing plates not present anymore on scratch and without report.zip" + # ) - else: - logging.info("Panoptes data not found for workflow entry: %s", row) + # for row in main_df.loc[ + # # (main_df["multiqc_scratch"] == False) + # (main_df["final_output_scratch"] == False) + # # & (main_df["report"] == False) + # ].to_dict("records"): + # logging.info(row) + + # # panoptes = True if row["status"] == "None" else False + # # panoptes = True + + # if dry_run == "False": + # if row["panoptes_id"] != "None": + # workflow_id = row["panoptes_id"] + # panoptes_data = [ + # e + # for e in workflows_data["workflows"] + # if e["id"] == workflow_id + # ] + # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' + # subprocess.run(command, shell=True, check=True) + + # process_new_directory( + # "/".join([path_to_watch, row["plate"]]), + # row["prefix"], + # row["sample"], + # row["plate_type"], + # report_only=False, + # panoptes=panoptes, + # ) + + logging.info( + "Processing plates without report.zip but with labels.tsv and still on scratch" + ) - logging.info( - "Updating /scratch files timestamps that are close to 6 months" - ) + for row in main_df.loc[ + (main_df["status"].str.contains("Report missing")) + ].to_dict("records"): + # for row in main_df.loc[ + # (main_df["final_output_scratch"] == True) + # & (main_df["scratch_rdays"] > 2) + # & (main_df["report_mc"] == False) + # ].to_dict("records"): + logging.info(row) - for row in main_df.loc[ - (main_df["final_output_scratch"] == True) - & (main_df["scratch_rdays"] < 10) - ].to_dict("records"): - logging.info(row) - self.update_timestamps( - f"{data_location}/{row['plate']}/{row['sample']}" + pipeline_updated = ( + "ashleys-qc-pipeline" + if "AQC" in row["status"] + else "mosaicatcher-pipeline" + ) + print(pipeline_updated) + + # panoptes = True if row["status"] == "None" else False + # panoptes = False + panoptes_entry = f"{pipeline}--{row['plate']}--{row['sample']}" + + if dry_run == "False": + process_new_directory( + "/".join([paths_to_watch[-1], row["plate"]]), + row["prefix"], + row["sample"], + row["plate_type"], + report_only=True, + panoptes=panoptes, + pipeline=pipeline_updated, ) - def process_new_directory( - self, + # if row["panoptes_id"] != "None": + # workflow_id = row["panoptes_id"] + # panoptes_data = [ + # e for e in workflows_data["workflows"] if e["id"] == workflow_id + # ][0] + + # if panoptes_data: + # command = f'sqlite3 /g/korbel2/weber/workspace/strandscape/.panoptes.db "DELETE FROM workflows WHERE id={workflow_id};"' + # subprocess.run(command, shell=True, check=True) + + # cursor.execute( + # """ + # INSERT INTO workflows (name, status, done, total, started_at, completed_at) + # VALUES (?, ?, ?, ?, ?, ?) + # """, + # ( + # panoptes_entry, + # "Done", + # panoptes_data["jobs_done"], + # panoptes_data["jobs_total"], + # panoptes_data["started_at"], + # panoptes_data["completed_at"], + # ), + # ) + # connection.commit() + + # else: + # logging.info("Panoptes data not found for workflow entry: %s", row) + + logging.info("Updating /scratch files timestamps that are close to 6 months") + + for row in main_df.loc[ + (main_df["final_output_scratch"] == True) & (main_df["scratch_rdays"] < 10) + ].to_dict("records"): + logging.info(row) + update_timestamps(f"{data_location}/{row['plate']}/{row['sample']}") + + +def process_new_directory( + directory_path, + prefix, + sample_name, + plate_type, + report_only=False, + panoptes=False, + pipeline="mosaicatcher-pipeline", +): + """Process the new directory, check for .txt.gz files and execute snakemake command if conditions are met.""" + + # Poll the directory until 576 files appear or a timeout is reached + timeout = 60 # Timeout in seconds + start_time = time.time() + + # while True: + # Count the number of .txt.gz files in the new directory + txt_gz_files = glob.glob(directory_path + "/*.txt.gz") + num_files = len(txt_gz_files) + + # # If the desired number of files is found or timeout is reached, break the loop + # if time.time() - start_time > timeout: + # break + + # # # # # Sleep for a while before the next poll + # time.sleep(5) # Sleep for 5 seconds + + # Process the found .txt.gz files + # process_txt_gz_files(directory_path, txt_gz_files, num_files) + execute_command( directory_path, prefix, sample_name, plate_type, - report_only=False, - panoptes=False, - ): - """Process the new directory, check for .txt.gz files and execute snakemake command if conditions are met.""" - - # Poll the directory until 576 files appear or a timeout is reached - timeout = 60 # Timeout in seconds - start_time = time.time() - - # while True: - # Count the number of .txt.gz files in the new directory - txt_gz_files = glob.glob(directory_path + "/*.txt.gz") - num_files = len(txt_gz_files) - - # # If the desired number of files is found or timeout is reached, break the loop - # if time.time() - start_time > timeout: - # break - - # # # # # Sleep for a while before the next poll - # time.sleep(5) # Sleep for 5 seconds + report_only=report_only, + panoptes=panoptes, + pipeline=pipeline, + ) - # Process the found .txt.gz files - # self.process_txt_gz_files(directory_path, txt_gz_files, num_files) - self.execute_command( - directory_path, - prefix, - sample_name, - plate_type, - report_only=report_only, - panoptes=panoptes, - ) - def execute_command( - self, - directory_path, - prefix, - sample, - plate_type, - report_only=False, - cell=None, - panoptes=False, - ): - """Execute the command.""" +def execute_command( + directory_path, + prefix, + sample, + plate_type, + report_only=False, + cell=None, + panoptes=False, + pipeline="mosaicatcher-pipeline", +): + """Execute the command.""" - # Change directory and run the snakemake command - date_folder = directory_path.split("/")[-1] + # Change directory and run the snakemake command + date_folder = directory_path.split("/")[-1] - ashleys_pipeline_only = True if pipeline == "ashleys-qc-pipeline" else False + ashleys_pipeline_only = True if pipeline == "ashleys-qc-pipeline" else False - genome_browsing_files_generation = ( - False if pipeline == "ashleys-qc-pipeline" else True - ) + genome_browsing_files_generation = ( + False if pipeline == "ashleys-qc-pipeline" else True + ) - year = date_folder.split("-")[0] - genecore_prefix = ( - f"{directory_path[0]}/{year}" - if year in ["2023", "2024"] - else paths_to_watch[0] - ) + year = date_folder.split("-")[0] + genecore_prefix_new_version = "/".join(directory_path.split("/")[:-1]) + genecore_prefix = ( + f"{genecore_prefix_new_version}/{year}" + if str(year) in ["2023", "2024"] + else paths_to_watch[0] + ) - cmd = [ - f"{snakemake_binary}", - "-s", - "workflow/Snakefile", - # "--set-resources", - # "ashleys_mark_duplicates:constraint='milan\|rome'", - "--config", - "genecore=True", - f"genecore_prefix={genecore_prefix}", - f"genecore_date_folder={date_folder}", - f"genecore_regex_element={prefix}", - f'samples_to_process="[{sample}]"', - f"plate_type={plate_type}", - "multistep_normalisation=True", - f"genome_browsing_files_generation={genome_browsing_files_generation}", - "MultiQC=True", - "split_qc_plot=False", - f"publishdir={publishdir_location}", - "email=thomas.weber@embl.de", - f"data_location={data_location}", - f"ashleys_pipeline_only={ashleys_pipeline_only}", - "ashleys_pipeline=True", - "--nolock", - "--rerun-incomplete", + cmd = [ + f"{snakemake_binary}", + "-s", + "workflow/Snakefile", + # "--set-resources", + # "ashleys_mark_duplicates:constraint='milan\|rome'", + "--config", + "genecore=True", + f"genecore_prefix={genecore_prefix}", + f"genecore_date_folder={date_folder}", + f"genecore_regex_element={prefix}", + f'samples_to_process="[{sample}]"', + f"plate_type={plate_type}", + "multistep_normalisation=True", + f"genome_browsing_files_generation={genome_browsing_files_generation}", + "MultiQC=True", + "split_qc_plot=False", + f"publishdir={publishdir_location}", + "email=thomas.weber@embl.de", + f"data_location={data_location}", + f"ashleys_pipeline_only={ashleys_pipeline_only}", + "ashleys_pipeline=True", + "--nolock", + "--rerun-incomplete", + "--rerun-triggers", + "mtime", + # "--touch", + ] + + if cell: + cmd = cmd[:-2] + [ + f"{data_location}/{date_folder}/{sample}/multiqc/fastqc/{cell}_1_fastqc.html", "--rerun-triggers", "mtime", - # "--touch", + "--force", ] - if cell: - cmd = cmd[:-2] + [ - f"{data_location}/{date_folder}/{sample}/multiqc/fastqc/{cell}_1_fastqc.html", - "--rerun-triggers", - "mtime", - "--force", - ] - - if report_only is False: - logging.info( - "Running command: %s", " ".join(cmd + profile_dry_run + dry_run_options) - ) - - process = subprocess.Popen( - cmd + profile_dry_run + dry_run_options, - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT, - universal_newlines=True, - cwd=working_directory, - env=my_env, - ) - - # Variable to store the penultimate line - penultimate_line = "" - - # Read the output line by line in real-time - for line in iter(process.stdout.readline, ""): - logging.info(line.strip()) # log line in real-time - if line.strip(): # If line is not blank - penultimate_line = line.strip() - - # Wait for the subprocess to finish - process.wait() - logging.info("Return code: %s", process.returncode) - dryrun_check = True if (str(process.returncode) == str(0)) else False - - else: - dryrun_check = True - - if dryrun_check is True: - self.run_second_command( - cmd, - profile_slurm, - data_location, - date_folder, - sample, - report_only, - cell, - panoptes, - ) - else: - logging.info("\nThe output is not as expected.") - - def run_second_command( - self, - cmd, - profile_slurm, - data_location, - date_folder, - sample, - report_only=False, - cell=None, - panoptes=False, - ): - """Run the second command and write the output to a log file.""" - - report_location = f"{publishdir_location}/{date_folder}/{sample}/reports/{sample}_{pipeline}_report.zip" - report_options = [ - "--report", - f"{report_location}", - "--report-stylesheet", - "/g/korbel2/weber/workspace/mosaicatcher-update/workflow/report/custom-stylesheet.css", - ] + if report_only is False: + logging.info( + "Running command: %s", " ".join(cmd + profile_dry_run + dry_run_options) + ) - wms_monitor_options = "http://127.0.0.1:8058" - run_id = f"{pipeline}--{date_folder}--{sample}" - wms_monitor_renaming_option = f"name={run_id}" + process = subprocess.Popen( + cmd + profile_dry_run + dry_run_options, + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT, + universal_newlines=True, + cwd=working_directory, + env=my_env, + ) - wms_monitor_args = [ - "--wms-monitor", - f"{wms_monitor_options}", - "--wms-monitor-arg", - f"{wms_monitor_renaming_option}", - ] + # Variable to store the penultimate line + penultimate_line = "" - # print(cmd + profile_slurm + report_options) + # Read the output line by line in real-time + for line in iter(process.stdout.readline, ""): + logging.info(line.strip()) # log line in real-time + if line.strip(): # If line is not blank + penultimate_line = line.strip() - os.makedirs(f"watchdog/logs/per-run/{pipeline}", exist_ok=True) + # Wait for the subprocess to finish + process.wait() + logging.info("Return code: %s", process.returncode) + dryrun_check = True if (str(process.returncode) == str(0)) else False - # Get the current date and time - now = datetime.now() + else: + dryrun_check = True - # Convert it to a string - current_time = now.strftime("%Y%m%d%H%M%S") + if dryrun_check is True: + run_second_command( + cmd, + profile_slurm, + data_location, + date_folder, + sample, + report_only, + cell, + panoptes, + pipeline, + ) + else: + logging.info("\nThe output is not as expected.") + + +def run_second_command( + cmd, + profile_slurm, + data_location, + date_folder, + sample, + report_only=False, + cell=None, + panoptes=False, + pipeline="mosaicatcher-pipeline", +): + """Run the second command and write the output to a log file.""" + + wms_monitor_options = "http://127.0.0.1:8058" + run_id = f"{pipeline}--{date_folder}--{sample}" + wms_monitor_renaming_option = f"name={run_id}" + + wms_monitor_args = [ + "--wms-monitor", + f"{wms_monitor_options}", + "--wms-monitor-arg", + f"{wms_monitor_renaming_option}", + ] + + # print(cmd + profile_slurm + report_options) + + os.makedirs( + f"watchdog/logs/per-run/{pipeline}/{date_folder}/{sample}", exist_ok=True + ) - if panoptes is True: - final_cmd = cmd + wms_monitor_args + profile_slurm - else: - final_cmd = cmd + profile_slurm - - if report_only is False: - logging.info("\nThe output is as expected.") - # logging.info("Running command: %s", " ".join(cmd + profile_slurm)) - - logging.info("Running command: %s", " ".join(final_cmd)) - - with open( - f"watchdog/logs/per-run/{pipeline}/{current_time}_{date_folder}_{sample}.log", - "w", - ) as f: - # process2 = subprocess.Popen(cmd + wms_monitor_args + profile_dry_run, stdout=f, stderr=f, universal_newlines=True, cwd=working_directory, env=my_env) - process2 = subprocess.Popen( - final_cmd, - stdout=f, - stderr=f, - universal_newlines=True, - cwd=working_directory, - env=my_env, - ) - process2.wait() + # Get the current date and time + now = datetime.now() - logging.info("Return code: %s", process2.returncode) + # Convert it to a string + current_time = now.strftime("%Y%m%d%H%M%S") - # Change the permissions of the new directory - # subprocess.run(["chmod", "-R", "777", f"{data_location}/{date_folder}"]) + if panoptes is True: + final_cmd = cmd + wms_monitor_args + profile_slurm + else: + final_cmd = cmd + profile_slurm - # if report_only is True: - # check_report = True - # else: - # check_report = True if (str(process2.returncode) == str(0)) else False + if report_only is False: + logging.info("\nThe output is as expected.") + # logging.info("Running command: %s", " ".join(cmd + profile_slurm)) - check_report = True + logging.info("Running command: %s", " ".join(final_cmd)) - if check_report is True: - logging.info("Generating ashleys report.") - os.makedirs(os.path.dirname(report_location), exist_ok=True) - # os.makedirs(f"{publishdir_location}/{date_folder}/{sample}/reports/", exist_ok=True) - logging.info( - "Running command: %s", " ".join(cmd + profile_dry_run + report_options) + log_file = f"/g/korbel2/weber/workspace/mosaicatcher-update/watchdog/logs/per-run/{pipeline}/{date_folder}/{sample}/{current_time}.log" + with open(log_file, "w") as f: + logging.info(f"Writing execution log to: {log_file}") + # process2 = subprocess.Popen(cmd + wms_monitor_args + profile_dry_run, stdout=f, stderr=f, universal_newlines=True, cwd=working_directory, env=my_env) + process2 = subprocess.Popen( + final_cmd, + stdout=f, + stderr=f, + universal_newlines=True, + cwd=working_directory, + env=my_env, ) - with open( - f"watchdog/logs/per-run/{pipeline}/{current_time}_{date_folder}_{sample}_report.log", - "w", - ) as f: - process2 = subprocess.Popen( - cmd + profile_dry_run + report_options, - stdout=f, - stderr=f, - universal_newlines=True, - cwd=working_directory, - env=my_env, - ) - # process2 = subprocess.Popen(cmd + profile_slurm + report_options, stdout=f, stderr=f, universal_newlines=True, cwd=working_directory, env=my_env) - process2.wait() - - logging.info("Return code: %s", process2.returncode) + process2.wait() - # ZIPFILE + logging.info("Return code: %s", process2.returncode) - import zipfile + # Change the permissions of the new directory + # subprocess.run(["chmod", "-R", "777", f"{data_location}/{date_folder}"]) - # Check if the file exists and is a valid zip file - if zipfile.is_zipfile(report_location): - # Specify the directory where you want to extract the contents - # If you want to extract in the same directory as the zip file, just use the parent directory - extract_location = ( - f"{publishdir_location}/{date_folder}/{sample}/reports/" - ) + if report_only is True: + check_report = True + else: + check_report = True if (str(process2.returncode) == str(0)) else False - # Extract the zip file - with zipfile.ZipFile(report_location, "r") as zip_ref: - zip_ref.extractall(extract_location) - print(f"Extracted the archive to {extract_location}") - else: - print(f"{report_location} is not a valid zip file.") + # check_report = True + print("check_report: ", check_report) - # Change the permissions of the new directory - subprocess.run(["chmod", "-R", "777", f"{data_location}/{date_folder}"]) + print("pipeline: ", pipeline) + pipeline_updated = "mosaicatcher-pipeline" + if check_report is False or pipeline == "ashleys-qc-pipeline": + pipeline_updated = "ashleys-qc-pipeline" -def main(): - # Create the event handler - event_handler = MyHandler() + ashleys_pipeline_only_updated = ( + True if pipeline_updated == "ashleys-qc-pipeline" else False + ) + ashleys_pipeline_only_real = True if pipeline == "ashleys-qc-pipeline" else False + print(cmd) + # Replace ashleys_pipeline_only in cmd by getting index of the element and replacing it + cmd[ + cmd.index(f"ashleys_pipeline_only={ashleys_pipeline_only_real}") + ] = f"ashleys_pipeline_only={ashleys_pipeline_only_updated}" + + report_location = f"{publishdir_location}/{date_folder}/{sample}/reports/{sample}_mosaicatcher-pipeline_report.zip" + report_options = [ + "--report", + f"{report_location}", + "--report-stylesheet", + "/g/korbel2/weber/workspace/mosaicatcher-update/workflow/report/custom-stylesheet.css", + ] + + logging.info("Generating report.") + os.makedirs(os.path.dirname(report_location), exist_ok=True) + os.makedirs( + f"watchdog/logs/per-run/{pipeline}/{date_folder}/{sample}", + exist_ok=True, + ) + # os.makedirs(f"{publishdir_location}/{date_folder}/{sample}/reports/", exist_ok=True) + logging.info( + "Running command: %s", " ".join(cmd + profile_dry_run + report_options) + ) - # Create an observer - observer = Observer() + log_file = f"/g/korbel2/weber/workspace/mosaicatcher-update/watchdog/logs/per-run/{pipeline}/{date_folder}/{sample}/{current_time}_report.log" + with open(log_file, "w") as f: + logging.info(f"Writing report execution log to: {log_file}") + + process2 = subprocess.Popen( + cmd + profile_dry_run + report_options, + stdout=f, + stderr=f, + universal_newlines=True, + cwd=working_directory, + env=my_env, + ) + # process2 = subprocess.Popen(cmd + profile_slurm + report_options, stdout=f, stderr=f, universal_newlines=True, cwd=working_directory, env=my_env) + process2.wait() - # Assign the observer to the path and the event handler - observer.schedule(event_handler, paths_to_watch[-1], recursive=False) + logging.info("Return code: %s", process2.returncode) - # Start the observer - observer.start() + # ZIPFILE - # Start the periodical directory scanning in a separate thread - def periodic_scan(): - while True: - # generate_data_file(publishdir_location) - event_handler.check_unprocessed_folder() - time.sleep(3600) # Scan the directory every hour + import zipfile - scan_thread = threading.Thread(target=periodic_scan) - scan_thread.start() + # Check if the file exists and is a valid zip file + if zipfile.is_zipfile(report_location): + # Specify the directory where you want to extract the contents + # If you want to extract in the same directory as the zip file, just use the parent directory + extract_location = f"{publishdir_location}/{date_folder}/{sample}/reports/" - try: - while True: - logging.info("Waiting for new plate ...") - time.sleep(3600) - except KeyboardInterrupt: - observer.stop() + # Extract the zip file + with zipfile.ZipFile(report_location, "r") as zip_ref: + zip_ref.extractall(extract_location) + print(f"Extracted the archive to {extract_location}") + else: + print(f"{report_location} is not a valid zip file.") - observer.join() + # Change the permissions of the new directory + subprocess.run(["chmod", "-R", "777", f"{data_location}/{date_folder}"]) if __name__ == "__main__": - main() + while True: + logging.info("Waiting for new plate ...") + check_unprocessed_folder() + time.sleep(3600) diff --git a/workflow/data/mm10.bin_200kb_all.bed b/workflow/data/mm10.bin_200kb_all.bed index b4e1897e..1fa614ce 100644 --- a/workflow/data/mm10.bin_200kb_all.bed +++ b/workflow/data/mm10.bin_200kb_all.bed @@ -1,13640 +1,13640 @@ -chr1 0 200000 -chr1 200000 400000 -chr1 400000 600000 -chr1 600000 800000 -chr1 800000 1000000 -chr1 1000000 1200000 -chr1 1200000 1400000 -chr1 1400000 1600000 -chr1 1600000 1800000 -chr1 1800000 2000000 -chr1 2000000 2200000 -chr1 2200000 2400000 -chr1 2400000 2600000 -chr1 2600000 2800000 -chr1 2800000 3000000 -chr1 3000000 3200000 -chr1 3200000 3400000 -chr1 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91600000 +chrY 91600000 91744698 diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index dcf2c15d..5b7fc757 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -332,7 +332,6 @@ class HandleInput: for e in os.listdir(thisdir) if e not in exclude and e.endswith(".zip") is False ] - # print(l_to_process) if config["samples_to_process"]: l_to_process = [ e for e in l_to_process if e in config["samples_to_process"] diff --git a/workflow/rules/count.smk b/workflow/rules/count.smk index 491f9daf..2d24391b 100755 --- a/workflow/rules/count.smk +++ b/workflow/rules/count.smk @@ -64,20 +64,41 @@ if config["ashleys_pipeline"] is False: > {log} 2>&1 """ - rule populate_counts: - input: - bin_bed=ancient("workflow/data/bin_200kb_all.bed"), - counts="{folder}/{sample}/counts/{sample}.txt.raw.gz", - output: - populated_counts="{folder}/{sample}/counts/{sample}.txt.populated.gz", - log: - "{folder}/log/plot_mosaic_counts/{sample}.log", - conda: - "../envs/mc_base.yaml" - resources: - mem_mb=get_mem_mb, - script: - "../scripts/utils/populated_counts_for_qc_plot.py" + if config["reference"] != "mm10": + + rule populate_counts: + input: + bin_bed=ancient("workflow/data/bin_200kb_all.bed"), + counts="{folder}/{sample}/counts/{sample}.txt.raw.gz", + output: + populated_counts="{folder}/{sample}/counts/{sample}.txt.populated.gz", + log: + "{folder}/log/plot_mosaic_counts/{sample}.log", + conda: + "../envs/mc_base.yaml" + resources: + mem_mb=get_mem_mb, + script: + "../scripts/utils/populated_counts_for_qc_plot.py" + + else: + + rule populate_counts: + input: + counts="{folder}/{sample}/counts/{sample}.txt.raw.gz", + output: + populated_counts="{folder}/{sample}/counts/{sample}.txt.populated.gz", + log: + "{folder}/log/plot_mosaic_counts/{sample}.log", + conda: + "../envs/ashleys_base.yaml" + resources: + mem_mb=get_mem_mb, + shell: + """ + zcat {input.counts} | awk 'BEGIN {{OFS="\t"}}; NR==1 {{print $0, "bin_id"}}; NR>1 {{print $0, $1 "_" $2 "_" $3}}' | \ + gzip > {output.populated_counts} + """ if config["input_bam_legacy"] is True: diff --git a/workflow/scripts/plotting/plot_clustering_dev_clean.R b/workflow/scripts/plotting/plot_clustering_dev_clean.R index e450dc9a..422669fb 100644 --- a/workflow/scripts/plotting/plot_clustering_dev_clean.R +++ b/workflow/scripts/plotting/plot_clustering_dev_clean.R @@ -143,10 +143,23 @@ col_annotation <- sapply(strsplit(lite_data_pivot_clustering$pos, "_"), `[`, 1) col_test <- factor(sapply(strsplit(colnames(t_lite_data_pivot_clustering_num), "_"), `[`, 1), levels = unique(sapply(strsplit(colnames(t_lite_data_pivot_clustering_num), "_"), `[`, 1))) + +calculate_lwd <- function(num_columns, min_columns = 30, max_columns = 500, min_lwd = 0.1, max_lwd = 1.5) { + # Linear interpolation + lwd <- (max_lwd - min_lwd) * (max_columns - num_columns) / (max_columns - min_columns) + min_lwd + # Ensure lwd is within the specified range + return(max(min(lwd, max_lwd), min_lwd)) +} + +# Usage: +num_columns <- ncol(t_lite_data_pivot_clustering_num) +lwd <- calculate_lwd(num_columns) + + cl_h <- Heatmap(as.matrix(t_lite_data_pivot_clustering_num), name = "LLR", col = RColorBrewer::brewer.pal(name = "Reds", n = 9), # column_title = "a discrete numeric matrix", - rect_gp = gpar(col = "white", lwd = 1.5), + rect_gp = gpar(col = "white", lwd = lwd), top_annotation = ComplexHeatmap::HeatmapAnnotation( foo = anno_block(gp = gpar(fill = 2:24)) ), @@ -231,7 +244,7 @@ col_test <- factor(sapply(strsplit(colnames(t_lite_data_pivot), "_"), `[`, 1), l cat_h <- Heatmap(as.matrix(t_lite_data_pivot), name = "SV type", col = colors, # column_title = "a discrete numeric matrix", - rect_gp = gpar(col = "white", lwd = 1.5), + rect_gp = gpar(col = "white", lwd = lwd), top_annotation = ComplexHeatmap::HeatmapAnnotation( foo = anno_block(gp = gpar(fill = 2:24)) ), diff --git a/workflow/scripts/plotting/qc.R b/workflow/scripts/plotting/qc.R index 65e0bc09..6f643aaf 100644 --- a/workflow/scripts/plotting/qc.R +++ b/workflow/scripts/plotting/qc.R @@ -156,9 +156,9 @@ if (add_overview_plot == T) { d_mv <- d[class != "None", .(mean = mean(w + c), var = var(w + c)), by = .(sample, cell)] print(d_mv) - if(nrow(d_mv) > 0) { + if (nrow(d_mv) > 0) { d_p <- d_mv[, .(p = sum(mean * mean) / sum(mean * var)), by = sample] - + ov_meanvar <- ggplot(d_mv) + geom_point(aes(mean, var), alpha = 0.4) + facet_wrap(~sample, nrow = 1) + @@ -168,7 +168,7 @@ if (add_overview_plot == T) { ggtitle("Mean variance relationship of reads per bin") + xlab("Mean") + ylab("Variance") - + # Arranging overview plot content <- ggdraw() + draw_plot(ov_binsizes, x = 0, y = .66, width = .5, height = .33) + @@ -177,7 +177,7 @@ if (add_overview_plot == T) { draw_plot(ov_meanvar, x = 0, y = 0, width = min(n_samples / 3, 1), height = .33) } else { print("d_mv is empty. Skipping the overview mean/variance plot...") - + # Arranging overview plot without ov_meanvar content <- ggdraw() + draw_plot(ov_binsizes, x = 0, y = .66, width = .5, height = .33) + @@ -216,8 +216,8 @@ if (add_overview_plot == T) { # Plot all cells for (s in unique(d$sample)) { - # for (ce in unique(d[sample == s, ]$cell)[3]) for (ce in unique(d[sample == s, ]$cell)) + # for (ce in unique(d[sample == s, ]$cell)[1:5]) { message(paste("* Plotting sample", s, "cell", ce)) @@ -242,8 +242,14 @@ for (s in unique(d$sample)) # print(e_lite, n = 40) # e_lite <- e + # print(e) + # print(e$bin_id) + # fill in missing bin_ids with "" + e$bin_id[is.na(e$bin_id)] <- "" + # print(e$bin_id) e_lite <- filter(e, bin_id == "") - print(e_lite) + # print("e_lite") + # print(e_lite) diff --git a/workflow/scripts/utils/update_counts.awk b/workflow/scripts/utils/update_counts.awk new file mode 100644 index 00000000..2e480124 --- /dev/null +++ b/workflow/scripts/utils/update_counts.awk @@ -0,0 +1,26 @@ +#!/usr/bin/awk -f + +BEGIN {OFS="\t"} + +NR==FNR { + norm[$1,$2,$3]=$5; + next +} + +FNR==1 { + if (NF < 10) { + print $0, "bin_id"; + add_bin_id = 1; + } else { + print $0; + } +} + +FNR>1 { + $8=(($1,$2,$3) in norm && norm[$1,$2,$3]!="good") ? "None" : $8; + if (add_bin_id) { + print $0, $1"_"$2"_"$3; + } else { + print $0; + } +}