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fastq screen killed, out of memory #187

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kelly-sovacool opened this issue Dec 17, 2024 · 0 comments · Fixed by #188
Closed

fastq screen killed, out of memory #187

kelly-sovacool opened this issue Dec 17, 2024 · 0 comments · Fixed by #188
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FASTQC_screen exceeded memory allocation and some processes were killed.
I have attached an excerpt from the .err file:

Using fastq_screen v0.13.0
Reading configuration from 'resources/biowulf/fastq_screen.conf'
Adding database Human
Adding database Mouse
Adding database Bacteria
Adding database Fungi
Adding database Virus
Using 32 threads for searches
Option --subset set to 1000000 reads
Processing 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz
Counting sequences in 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz
Making reduced sequence file with ratio 53:1
Searching 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz_temp_subset.fastq against Human
Searching 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz_temp_subset.fastq against Mouse
Searching 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz_temp_subset.fastq against Bacteria
Aligner warning: Killed
Aligner warning: (ERR): bowtie2-align exited with value 137
Searching 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz_temp_subset.fastq against Fungi
Aligner warning: Killed
Aligner warning: (ERR): bowtie2-align exited with value 137
Searching 2237CHLT1_19706269_S7_L001_001.R1.trim.fastq.gz_temp_subset.fastq against Virus
...
Processing complete
@kopardev kopardev added the RENEE RepoName label Dec 17, 2024
@kelly-sovacool kelly-sovacool added bug Something isn't working and removed RENEE RepoName labels Dec 17, 2024
kelly-sovacool added a commit that referenced this issue Dec 19, 2024
@kelly-sovacool kelly-sovacool self-assigned this Dec 19, 2024
@kelly-sovacool kelly-sovacool added this to the 2024-12 milestone Dec 19, 2024
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