search

EichlerLab / isoseq_pipeline

Isoform detection with paralog-specific partitioning
2 stars 0 forks source link

failure at "clean fastq" step #4

Closed mldough closed 7 years ago

mldough commented 7 years ago

Pipeline fails at rule clean_fastq. Returns error message like:

Error in job clean_fastq while creating output file partitioned/adult_brain/333/isoseq_flnc.q40pass.cleaned.fastq.
RuleException:
CalledProcessError in line 113 of /net/eichler/vol21/projects/human_primate_brain_ips_transcriptomes/nobackups/pacbio_data/brad_pipeline_test/2016-12-23-full_test_adult_and_fetal_q40_unmapped_also/isoseq_pipeline/tofu.partition.snake:
Command 'module load anaconda/20161130
        export PATH=/net/eichler/vol2/eee_shared/modules/anaconda3/envs/py3.20161130/bin/:$PATH
        python clean_fastq.py partitioned/adult_brain/333/isoseq_flnc.q40pass.fastq partitioned/adult_brain/333/isoseq_flnc.q40pass.cleaned.fastq' returned non-zero exit status -9
  File "/net/eichler/vol21/projects/human_primate_brain_ips_transcriptomes/nobackups/pacbio_data/brad_pipeline_test/2016-12-23-full_test_adult_and_fetal_q40_unmapped_also/isoseq_pipeline/tofu.partition.snake", line 113, in __rule_clean_fastq
  File "/net/eichler/vol2/eee_shared/modules/anaconda3/envs/py3.20161130/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Exiting because a job execution failed. Look above for error message

Running command interactively works.

mldough commented 7 years ago

This actually is a memory issue—can be resolved by increasing memory requested to > 5x the size of the fastq file. Can also monitor memory usage while running to check with htop.