Trackhub stuff
See original GitHub issueWhen 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:
- Created 4 years ago
- Reactions:1
- Comments:11 (7 by maintainers)
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Ill try the fix in the afternoon, thanks!
pinging @siebrenf since he worked on it last and might have an idea