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sheffield-bioinformatics-core / periscope

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.
GNU General Public License v3.0
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snakefile error /bin/bash: bc: command not found split: invalid number of lines: #39

Open Viromic opened 2 years ago

Viromic commented 2 years ago

/bin/bash: bc: command not found split: invalid number of lines: ?

RuleException: CalledProcessError in line 104 of /opt/conda/envs/periscope/lib/python3.6/site-packages/periscope/scripts/Snakefile: Command ' set -euo pipefail; samtools view -H omicrons.bam > omicrons_header.txt && samtools view omicrons.bam > omicrons.sam && split -d -l $(echo wc -l omicrons.sam | cut -f1 -d " " /1+1 | bc) omicrons.sam omicrons.split. ' returned non-zero exit status 1. File "/opt/conda/envs/periscope/lib/python3.6/site-packages/periscope/scripts/Snakefile", line 104, in __rule_split File "/opt/conda/envs/periscope/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job split since they might be corrupted:

Viromic commented 2 years ago

a samtools problem ?

mattdmem commented 2 years ago

either samtools or not enough reads to split maybe? odd that it can't find bc though - what are you running this on?

Viromic commented 2 years ago

it is a galaxy instance and the set cases is some 132 high quality singles but we cant really figure this bc nor samtools split for the omicrons to distinguish the sister cladesK21 (and L21 BA.1 and BA.2 lineages as they emerge ) out here properly at both levels i.e protein and corresponding rna in terms of recombinatorial events and secondary structures will have to resort to the BAMs https://observablehq.com/@spond/ba1-selection

Perhaps periscope might be a god candidate for https://workflowhub.eu/workflows perhaps ?