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USDA-VS / vSNP3

vSNP -- validate SNPs
GNU General Public License v3.0
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Error while running vSNP 3.20 "step1" with nanopore data #7

Open duceppemo opened 4 months ago

duceppemo commented 4 months ago

Command used: vsnp3_step1.py \ -r1 "$r1" \ --spoligo \ --nanopore

Error message: Traceback (most recent call last): File "/home/bioinfo/miniconda3/envs/vsnp3.20/bin/vsnp3_step1.py", line 273, in <module> vsnp.run() File "/home/bioinfo/miniconda3/envs/vsnp3.20/bin/vsnp3_step1.py", line 158, in run if alignment.zero_coverage.ave_coverage < 40 or alignment.DUPLICATION_RATIO > .80 or float(fastq_stats.R1.passQ20) < 50.0: ValueError: could not convert string to float: '11,015' Looks like it's caused by the use of a comma (",") as thousands separator. It might be link to the host system language preferences if you don't get that error on your dev / production machine.

duceppemo commented 4 months ago

Or it could be the decimal separator too. French keyboards used the comma and decimal separator. I definitely don't have 11,015X coverage, so it would make more sense that it's the decimal separator.

stuber commented 4 months ago

I've seen something similar. Try this and let's see if it fixes it.

Before running the script run export LC_ALL=C? Will look something like this.

export LC_ALL=C

vsnp3_step1.py -r1 *_R1*fastq.gz -r *_R2*fastq.gz
stuber commented 4 months ago

Also, I see you're using the --nanopore option. With this option bcftools is used. bcftools has not been working from conda lately. If you have issues with it let me know and I'll send what I've used to fix it.