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KarchinLab / 2020plus

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
http://2020plus.readthedocs.org
Apache License 2.0
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Keep getting error : Error in job simMaf while creating output file #9

Closed sandaru closed 5 years ago

sandaru commented 5 years ago

Hi I'm getting following error while executing sample files. I couldn't find any fix for this. Can you please help on this

ERROR:

snakemake -s Snakefile pretrained_predict -p --cores 1 \

 --config mutations="data/bladder.txt" output_dir="output_bladder" trained_classifier="data/2020plus_10k.Rdata"

Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 features 1 finishSim 1 og 1 predict_test 1 pretrained_predict 10 simFeatures 10 simMaf 10 simOg 10 simSummary 10 simTsg 1 summary 1 tsg 57

rule simMaf: input: data/bladder.txt output: output_bladder/simulated_summary/chasm_sim_maf3.txt jobid: 50 wildcards: iter=3

mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=$((342)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf3.txt Command: /root/miniconda3/envs/2020plus/bin/mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=126 -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf3.txt There were 832 indels identified. Kept 33771 mutations after droping mutations with missing information (Droped: 0) Dropped 832 mutations after only keeping Missense_Mutation, Silent, Nonsense_Mutation, Splice_Site, Nonstop_Mutation, Translation_Start_Site. Indels are processed separately. Dropped 182 mutations after only keeping valid SNVs Dropped 0 mutations when removing duplicates Working on chromosome: chr1 . . . Finished working on chromosome: chr1. Working on chromosome: chr19 . . . Finished working on chromosome: chr19. Working on chromosome: chr11 . . . Finished working on chromosome: chr11. Working on chromosome: chr2 . . . Finished working on chromosome: chr2. Working on chromosome: chr17 . . . Finished working on chromosome: chr17. Working on chromosome: chr3 . . . Finished working on chromosome: chr3. Working on chromosome: chr6 . . . Finished working on chromosome: chr6. Working on chromosome: chr12 . . . Finished working on chromosome: chr12. Working on chromosome: chr7 . . . Finished working on chromosome: chr7. Working on chromosome: chr5 . . . Finished working on chromosome: chr5. Working on chromosome: chr14 . . . Finished working on chromosome: chr14. Working on chromosome: chr16 . . . Finished working on chromosome: chr16. Working on chromosome: chr9 . . . Finished working on chromosome: chr9. Working on chromosome: chrX . . . Finished working on chromosome: chrX. Working on chromosome: chr10 . . . Finished working on chromosome: chr10. Working on chromosome: chr4 . . . Finished working on chromosome: chr4. Working on chromosome: chr8 . . . Finished working on chromosome: chr8. Working on chromosome: chr15 . . . Finished working on chromosome: chr15. Working on chromosome: chr20 . . . Finished working on chromosome: chr20. Working on chromosome: chr22 . . . Finished working on chromosome: chr22. Working on chromosome: chr13 . . . Finished working on chromosome: chr13. Working on chromosome: chr18 . . . Finished working on chromosome: chr18. Working on chromosome: chr21 . . . Finished working on chromosome: chr21. Working on chromosome: chrY . . . Finished working on chromosome: chrY. Working on chromosome: chrM . . . Finished working on chromosome: chrM. /bin/bash: line 1: 11394 Killed mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=$((342)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf3.txt *Error in job simMaf while creating output file output_bladder/simulated_summary/chasm_sim_maf3.txt. RuleException: CalledProcessError in line 135 of /root/Desktop/2020_Prod/2020plus-1.2.2/Snakefile: Command 'mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=$((342)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf3.txt' returned non-zero exit status 137. File "/root/Desktop/2020_Prod/2020plus-1.2.2/Snakefile", line 135, in __rule_simMaf File "/root/miniconda3/envs/2020plus/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job simMaf since they might be corrupted: output_bladder/simulated_summary/chasm_sim_maf3.txt Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message**

ctokheim commented 5 years ago

Hi. Based on "/bin/bash: line 1: 11394 Killed" in the error message, I suspect that 20/20+ exceeded your computer resources, such as memory or something else, and this resulted in the operating system killing the job. Are you running 20/20+ inside a virtual machine with limited resources? Regardless, it may be better to run 20/20+ on a computer cluster which has more resources.