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createIndices

See original GitHub issue

Hi everyone, I am new here 😃 I am trying to use this tool for ATAC-seq analysis on Catalina OS. in the first step createIndices i am getting the following error message:

Error in rule createGenomeFasta:
    jobid: 0
    output: /Users//Desktop/snakepipe/genome_fasta/genome.fa

RuleException:
OSError in line 11 of /Users/ta/opt/miniconda3/envs/snakePipes/lib/python3.6/site-packages/snakePipes/shared/rules/createIndices.snakefile:
[Errno 22] Invalid argument
  File "/Users/ta/opt/miniconda3/envs/snakePipes/lib/python3.6/site-packages/ta/shared/rules/createIndices.snakefile", line 33, in __rule_createGenomeFasta
  File "/Users/ta/opt/miniconda3/envs/snakePipes/lib/python3.6/site-packages/snakePipes/shared/rules/createIndices.snakefile", line 11, in downloadFile
  File "/Users/ta/opt/miniconda3/envs/snakePipes/lib/python3.6/tempfile.py", line 485, in func_wrapper
  File "/Users/ta/opt/miniconda3/envs/snakePipes/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message

I dont know what could be went wrong

thanks for your help TA

Issue Analytics

State:
Created 4 years ago
Comments:82 (29 by maintainers)

Top GitHub Comments

1reaction

GinaRecommented, Nov 25, 2019

I have tested DNA-mapping in a single-hybrid version now and run into similar issues as you did. For now this is an open issue we will try to fix it in a next release.

1reaction

steffenheynecommented, Nov 21, 2019

sorry do not delete createIndices output dir, I meant the DNA-mapping dir

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