I got the following error while running the example dataset. The file 2R.mpileup.log is empty - possibly a problem with fifo. System administrator checked and mkfifo is definitely installedon the system being used. The version installed is 8.28.
System administrator also tried recreating the software (running the snakemake pipeline) on another of our development machines and hit other problems with packages that are definitely installed but it doesn’t seem to like it.
I'm currently testing the popoolation2 part by running each step separately from command line.
Activating conda environment: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/conda/5af75ca214322542d38ca9626894a8ef
mkfifo: cannot create fifo 'results/mpileup/filt/pop2/pop2.2R.mpileup': Operation not permitted
[Mon Dec 6 12:29:00 2021]
Error in rule mpileup_popoolation_filter_indels:
jobid: 27
output: results/mpileup/filt/pop2/pop2.2R.mpileup, results/mpileup/filt/pop2/pop2.2R.mpileup.gz
log: results/mpileup/filt/pop2/pop2.2R.mpileup.log (check log file(s) for error message)
conda-env: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/conda/5af75ca214322542d38ca9626894a8ef
shell:
mkfifo results/mpileup/filt/pop2/pop2.2R.mpileup
(cat results/mpileup/filt/pop2/pop2.2R.mpileup | gzip --fast > results/mpileup/filt/pop2/pop2.2R.mpileup.gz &)
perl src/popoolation_1.2.2/basic-pipeline/filter-pileup-by-gtf.pl --input <(gzip --decompress --stdout results/mpileup/raw/pop2/pop2.2R.mpileup.gz) --gtf results/mpileup/filt/pop2/pop2.2R.gtf --output results/mpileup/filt/pop2/pop2.2R.mpileup 2> results/mpileup/filt/pop2/pop2.2R.mpileup.log 1>&2
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
[Mon Dec 6 12:29:03 2021]
Finished job 6.
33 of 71 steps (46%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/dyern/lstm_scratch/smsk_popoolation/.snakemake/log/2021-12-06T122740.426984.snakemake.log