xcor not completing on Sherlock singularity about atac-seq-pipeline HOT 14 CLOSED

Please upload a tar ball of all logs.

from atac-seq-pipeline.

Thanks! For all tasks or just the xcor?

from atac-seq-pipeline.

Please run this on your working directory.

$ find . -type f -name 'stdout' -or -name 'stderr' -or -name 'script' -or \
-name '*.qc' -or -name '*.txt' -or -name '*.log' -or -name '*.png' -or -name '*.pdf' \
| xargs tar -zcvf debug_[ISSUE_ID].tar.gz

from atac-seq-pipeline.

Thanks, here it is:
debug_34.tar.gz

from atac-seq-pipeline.

It failed to find a shared library for R.

PID=32489: Decompressing ChIP file
PID=32489: Loading required package: caTools
PID=32489: Error in dyn.load(file, DLLpath = DLLpath, ...) :
PID=32489:   unable to load shared object '/home/users/knoedler/R/x86_64-pc-linux-gnu-library/3.2/bitops/libs/bitops.so':
PID=32489:   libimf.so: cannot open shared object file: No such file or directory
PID=32489: Error: package 'caTools' could not be loaded
PID=32489: Execution halted

What was your full command line to run a pipeline? Can you upload your ~/.bashrc too?

from atac-seq-pipeline.

I see - is this a version issue (I think default R on sherlock is 3.4)? It looks like all the files are in my directory

from atac-seq-pipeline.

Oh, caTools isn't in R version 3.2 on my partition. That might be the problem.

from atac-seq-pipeline.

@knoedlerj: You are using singularity so the pipeline should not use anything locally installed on your home. What is your full command line? Also please upload workflow_opts/sherlock.json too.

from atac-seq-pipeline.

Command line is copy-pasted from Github:
INPUT=examples/sherlock/ENCSR356KRQ_subsampled_sherlock.json
java -jar -Dconfig.file=backends/backend.conf -Dbackend.default=slurm_singularity cromwell-34.jar run atac.wdl -i ${INPUT} -o workflow_opts/sherlock.json

(changed json to a txt file because github wouldn't let me attach as json for some reason)

sherlock.json.txt

from atac-seq-pipeline.

Please try with this backend file instead of backends/backend.conf.

backend_singularity_home_fix.conf.txt

from atac-seq-pipeline.

Thanks!! I'll give it a try.

from atac-seq-pipeline.

Ran everything but atacqc that time; thanks!

from atac-seq-pipeline.

@knoedlerj that sounds good but what kind of error did you get at ATAQC?

from atac-seq-pipeline.

Thanks, I actually fixed it - for some reason on Sherlock2 the macs2 and ataqc jobs fail to submit with a 'required node configuration not available' error with the default memory settings. I can't for the life of me figure out what's different about those jobs, but if I change the memory allocation from 20000 MB to 16000 MB it works.

from atac-seq-pipeline.