FileNotFoundException when fitting exponential model on cli

[burgerga]

When I run a commandline config with exponential model fit I get

(base) gerhard@upr ~ $  INSTALL4J_ADD_VM_PARAMS="-Xmx500G" bmdexpress2-cmd analyze --config-file ~/bmdx_test_config.json
import expression: /home/gerhard/BMD_count_CSSYN_PHH2D_SYN1_TP24conc_response.txt
Starting Williams Trend Test
Finished Williams Trend Test
bmd analysis on group williams
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21802400710_24248upr2696277524672132_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21494958434_24248upr27534711857115695_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21132104129_24248upr862602051717196_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2267596202_24248upr816134085488014_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2833231291_24248upr810427162126538208_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2738346097_24248upr801660182138718258_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2318320959_24248upr2584505712986930_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21646843425_24248upr18123692311051721404_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21083753281_24248upr2571379421597358_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2739742041_24248upr1293834529593102353_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21624359708_24248upr14073747531793217007_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2467817768_24248upr1407374757614294765_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2839864823_24248upr1407398782390881095_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21504783399_24248upr1407399739716217959_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2790902656_24248upr14074064681281080561_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M22016240436_24248upr1850697769656933702_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21341893642_24248upr18515199041860641039_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21889872668_24248upr2138661875805507055_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2421969240_24248upr78788932895988278_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21377100163_24248upr2138661849325434277_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2169844963_24248upr1660867244931463277_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M21822763027_24248upr1660867338678396850_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M2310223748_24248upr2097012900490351970_exponential.out (No such file or directory)
Input file problem: java.io.FileNotFoundException: /local/gerhard/gerhard-24248-upr/M28089121_24248upr782805361316109467_exponential.out (No such file or directory)
... (and so on)

First I thought it was because I had set tmpFolder, but that was not the case, also without tmpFolder set I get these messages.

I can find the exponential model results in the resulting bm2 however, so I'm not sure if this is actually a problem, but I just wanted to let you know.

For completeness my json:
bmdx_default_config.json.txt

[jamlover]

I am having the same problem, but also see exponential results in my output .bm2 file. I note that using basically the exact same configuration file on one other similar data set did not result in this type of error, while in a third case, it did.

Command and terminal output, all the way to completion, is pasted below.

$ /data/progs/BMDExpress2v502/bmdexpress2-cmd analyze --config-file=bmd-config.json
import expression: /data/hts2/John/Pthalates/dbp/genome_mapping/dbp.filtered.normFinal.sansD01.txt
Starting One-way ANOVA on dbp
Finished One-way ANOVA on dbp
Starting Williams Trend Test on dbp
Finished Williams Trend Test on dbp
bmd analysis on dbp_williams from group williams
Input file problem: java.io.FileNotFoundException: /home/jmartins/bmdexpress2/tmp/M21948466505_20244d2626ujmartins4aaadepagov17251870711145603843_exponential.out (No such file or directory)
selectBest1Model()
DEFINED analysis on dbp_williams_bmds
probe file=/data/hts2/John/Probes.txt
category file=/data/hts2/John/GOcategories_bpOnly.txt

[mark-liddell]

I'm also getting this issue

[jamlover]

Mark, I spoke with someone recently who is familiar with the development of BMDExpress and he told me this issue is safe to ignore. (He offered to tell me exactly what was causing it but because we had a time constraint on our meeting I told him that wasn't necessary).

[mark-liddell]

Cheers @jamlover, that gives me some piece of mind that this exceptions won't affect my outputs!

[auerbachs]

Apologies all for the extremely slow responses. I am not getting the alerts when people post issues. Just wanted to let you know that there is a new version of BMDExpress available and we will be working through the issues you noted if they have not already been addressed in version 3.

https://github.com/auerbachs/BMDExpress-3/releases