Error running MAGeCK-VISPR test data

[AGV_1969]

Hi eveyone,

I was trying to run MAGeCK-VISPR on test data available as "esc-testdata". I have successfully initialize the workflow and got "README.txt", "Snakefile" and "config.yaml" in working directory. After this, I execute "snakemake --cores 8" and I got this error:

*Error in job mageck_mle while creating output files results/test/ESC-MLE.gene_summary.txt, results/test/ESC-MLE.sgrna_summary.txt. 
RuleException: 
CalledProcessError in line 125 of /home/bioinfo/Descargas/esc-test/Snakefile: 
Command 'mageck mle --output-prefix results/test/ESC-MLE --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0  --count-table results/count/all.count.txt --design-matrix esc-testdata/designmatrix.txt 2> logs/mageck/test/ESC-MLE.log' returned non-zero exit status 1 
  File "/home/bioinfo/Descargas/esc-test/Snakefile", line 125, in __rule_mageck_mle 
  File "/home/bioinfo/miniconda3/lib/python3.5/concurrent/futures/thread.py", line 55, in run 
Will exit after finishing currently running jobs. 
Exiting because a job execution failed. Look above for error message*

Can you help me?

Thanks in advance for you excellent work.

Alberto

[Johannes Köster]

Thanks for reporting. Can you please post the output of the logfile logs/mageck/test/ESC-MLE.log?

[AGV_1969]

Hi Johannes. Thanks for your help!

This is the output of the logfile:

INFO @ Thu, 01 Sep 2016 20:30:42: Parameters: /home/bioinfo/miniconda3/bin/mageck mle --output-prefix results/test/ESC-MLE --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0 --count-table results/count/all.count.txt --design-matrix esc-testdata/designmatrix.txt INFO @ Thu, 01 Sep 2016 20:30:42: Cannot parse design matrix as a string; try to parse it as a file name ... INFO @ Thu, 01 Sep 2016 20:30:42: Design matrix: INFO @ Thu, 01 Sep 2016 20:30:42: [[ 1. 0.] INFO @ Thu, 01 Sep 2016 20:30:42: [ 1. 1.] INFO @ Thu, 01 Sep 2016 20:30:42: [ 1. 1.]] INFO @ Thu, 01 Sep 2016 20:30:42: Beta labels:baseline,esc INFO @ Thu, 01 Sep 2016 20:30:42: Included samples:plasmid,esc1,esc2 Traceback (most recent call last): File "/home/bioinfo/miniconda3/bin/mageck", line 65, in <module> main(); File "/home/bioinfo/miniconda3/bin/mageck", line 42, in main args=crisprseq_parseargs(); File "/home/bioinfo/miniconda3/lib/python3.5/site-packages/mageck/argsParser.py", line 160, in crisprseq_parseargs mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command File "/home/bioinfo/miniconda3/lib/python3.5/site-packages/mageck/mlemageck.py", line 56, in mageckmle_main from mageck.mleinstanceio import read_gene_from_file,write_gene_to_file,write_sgrna_to_file File "/home/bioinfo/miniconda3/lib/python3.5/site-packages/mageck/mleinstanceio.py", line 8, in <module> from mageck.mleclassdef import * File "/home/bioinfo/miniconda3/lib/python3.5/site-packages/mageck/mleclassdef.py", line 6, in <module> from IPython.core.debugger import Tracer ImportError: No module named 'IPython'

[Johannes Köster]

Hi, this looks like an error in your mageck version. Did you install mageck via conda? Which version are you using? Pinging @davidliwei.

[Wes Horton]

Our group experienced the same problem. We installed everything following the instructions on the home page.

mageck -v
mageck 0.5.4

While not a permanent fix, a member of our group figured out that it's caused (at least for us) by line 6 from /my/path/miniconda3/lib/python3.5/site-packages/mageck/mleclassdef.py
the line in question is: from IPython.core.debugger import Tracer.

We commented out that line and everything has run smoothly since.

[Johannes Köster]

@davidliwei is this already fixed in a newer mageck version?

[Wei Li]

I fixed it in the bitbucket commits several weeks ago. How to fix this in the pipeline? @johanneskoester

[sagar Utturkar]

I am trying this with "esc-testdata" as: snakemake --cores 10 and got the similar error as below:

Error in job mageck_mle while creating output files results/test/ESC-MLE.gene_summary.txt, results/test/ESC-MLE.sgrna_summary.txt.
RuleException:
CalledProcessError in line 151 of /scratch/snyder/s/sutturka/MAGIC_VISPR_test/esc-testdata/Snakefile:
Command 'mageck mle --norm-method median --output-prefix results/test/ESC-MLE --sgrna-eff-name-column 3 --sgrna-eff-score-column 4 --sgrna-efficiency annotation/sgrnas.bed --genes-var 0  --count-table results/count/all.count.txt --design-matrix /scratch/snyder/s/sutturka/MAGIC_VISPR_test/esc-testdata/designmatrix.txt 2> logs/mageck/test/ESC-MLE.log' returned non-zero exit status 255.
  File "/scratch/snyder/s/sutturka/MAGIC_VISPR_test/esc-testdata/Snakefile", line 151, in __rule_mageck_mle
  File "/group/bioinfo/apps/apps/miniconda-4.3.21/envs/mageck-vispr/lib/python3.6/concurrent/futures/thread.py", line 55, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

[Wei Li]

Can you check the log file about the error message: logs/mageck/test/ESC-MLE.log

[sagar Utturkar]

Thank you for pointing to the log file. In log file it was an error related to sample name:
ERROR @ Thu, 09 Nov 2017 14:16:09: Sample esc1 cannot be found on the original read count table results/count/all.count.txt.

I checked and found a typo in sample name. Thank you for the help.