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When running the RNAseq pipeline with my own fastq files and genome, the trackhub rule crashes:

rule trackhub:
    input: <TBD>
    output: /home/jsmits/Epithelial_fate_KC_LSC/RNA/trackhub
    log: /home/jsmits/Epithelial_fate_KC_LSC/RNA/log/trackhub/trackhub.log
    jobid: 4
    benchmark: /home/jsmits/Epithelial_fate_KC_LSC/RNA/benchmark/trackhub/trackhub.benchmark.txt

It seems to fail to generate the proper input, and therefore crashes a little time later:

INFO:snakemake.logging:[Tue Feb 25 12:08:57 2020]
Error in rule trackhub:
ERROR:snakemake.logging:Error in rule trackhub:
    jobid: 0
ERROR:snakemake.logging:    jobid: 0
    output: /home/jsmits/Epithelial_fate_KC_LSC/RNA/trackhub
ERROR:snakemake.logging:    output: /home/jsmits/Epithelial_fate_KC_LSC/RNA/trackhub
    log: /home/jsmits/Epithelial_fate_KC_LSC/RNA/log/trackhub/trackhub.log (check log file(s) for error message)
ERROR:snakemake.logging:    log: /home/jsmits/Epithelial_fate_KC_LSC/RNA/log/trackhub/trackhub.log (check log file(s) for error message)
ERROR:snakemake.logging:
RuleException:
AttributeError in line 501 of /home/jsmits/snakemake-workflows/rules/trackhub.smk:
'InputFiles' object has no attribute 'twobits'
  File "/home/jsmits/snakemake-workflows/rules/trackhub.smk", line 501, in __rule_trackhub
  File "/home/jsmits/anaconda3/envs/snakemake-workflows/lib/python3.6/concurrent/futures/thread.py", line 56, in run
ERROR:snakemake.logging:RuleException:
AttributeError in line 501 of /home/jsmits/snakemake-workflows/rules/trackhub.smk:
'InputFiles' object has no attribute 'twobits'
  File "/home/jsmits/snakemake-workflows/rules/trackhub.smk", line 501, in __rule_trackhub
  File "/home/jsmits/anaconda3/envs/snakemake-workflows/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
ERROR:snakemake.logging:Exiting because a job execution failed. Look above for error message

Issue Analytics

  • State:closed
  • Created 4 years ago
  • Reactions:1
  • Comments:11 (7 by maintainers)

github_iconTop GitHub Comments

1reaction
JGASmitscommented, Feb 25, 2020

Ill try the fix in the afternoon, thanks!

1reaction
Maarten-vd-Sandecommented, Feb 25, 2020

pinging @siebrenf since he worked on it last and might have an idea

Read more comments on GitHub >

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