Error in job annotate_sgrnas while creating output file annotation/sgrnas.bed.

[Sandra Schick]

Hi,

I receive the same error as mentioned in issue #4 for one of our datasets.

Error in job annotate_sgrnas while creating output file annotation/sgrnas.bed.
RuleException:
CalledProcessError in line 83 of /scratch/.../Snakefile:
Command 'mageck-vispr annotate-library ./Human_GeCKOv2_Library.csv --sgrna-len 20 --assembly hg38 > annotation/sgrnas.bed 2> logs/annotation/sgrnas.log' returned non-zero exit status 1
  File "/scratch/.../Snakefile", line 83, in __rule_annotate_sgrnas
  File "/cm/shared/apps/miniconda3/lib/python3.5/concurrent/futures/thread.py", line 55, in run

I have tried it several times on different days, but the error always comes. Do you have any suggestion?

[Sandra Schick]

It was now running on subsets of the dataset, but if I run the whole set, it still does not work:

Error in job mageck_count while creating output files results/count/all.count.txt, results/count/all.count_normalized.txt, results/count/all.countsummary.txt. RuleException: CalledProcessError in line 69 of /scratch/.../Snakefile: Command 'mageck count --output-prefix results/count/all --list-seq ./Human_GeCKOv2_Library_combine.csv --fastq X.fastq,Y.fastq Z.fastq --sample-label XY,YZ,XZ --trim-5 0 --sgrna-len 20 2> logs/mageck/count/all.log' returned non-zero exit status 1 File "/scratch/.../Snakefile", line 69, in __rule_mageck_count File "/cm/shared/apps/miniconda3/lib/python3.5/concurrent/futures/thread.py", line 55, in run

Do you have any idea where the error is?

[Johannes Köster]

Can you please post the log file logs/annotation/sgrnas.log?

[Sandra Schick]

Hi Johannes,

thanks a lot for your reply. I unfortunately don't have the log file anymore, where it did not run. It has worked for me now. The second problem was likely due to lack of memory.

[Johannes Köster]

Ok, sorry for the late reply!

[minette]

hello,

i have this error message, what should I do?

Error in job trim while creating output files 10031869_S1_R2_001_trim.fastq.gz, 10031869_S1_R2_001_trim_unp.fastq.gz. RuleException: CalledProcessError in line 36 of /home/douaa/test/trimmomatic.rule: Command 'java -jar -Xmx10000m /opt/Trimmomatic-0.33/trimmomatic-0.33.jar PE -threads 2 -phred33 Examples_fastqFiles/10031869_S1_R2_001.fastq.gz Trimming//10031869_S1_R2_001_trim.fastq.gz Trimming//10031869_S1_R2_001_trim_unp.fastq.gz ILLUMINACLIP/opt/Trimmomatic-0.33/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:9 ' returned non-zero exit status 1. File "/home/douaa/test/trimmomatic.rule", line 36, in __rule_trim File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 55, in run

thanks!