Error in rule sniffles_call

[EEsdaile]

Well, I'm back. I'm getting an error in the sniffles_call rule and I can't figure out why. Looks like the conda environment loaded correctly but sniffles is failing. Any suggestions?

snakemake.log Unlimited resources: walltime, mem Job counts: count jobs 1 SV_length_plot 1 SV_plot_carriers 1 alignment_stats 2 annotate_vcf 1 bcftools_reheader_sniffles 1 fast 1 filter_svim 1 npinv 1 sniffles_call 1 sniffles_genotype 2 sort_vcf 3 survivor 1 svim_call 17

rule sniffles_call: input: out/minimap2/alignment/sample.bam output: out/minimap2/sniffles_calls/sample.vcf log: log/minimap2/sniffles_call/sample.log jobid: 17 wildcards: aligner=minimap2, sample=sample resources: mem=2000, walltime=120

sniffles --mapped_reads out/minimap2/alignment/sample.bam --vcf out/minimap2/sniffles_calls/sample.vcf --threads 1 2> log/minimap2/sniffles_call/sample.log Activating conda environment /home/esdaile/long_read/nano-snakemake/.snakemake/conda/b827a74e. Error in rule sniffles_call: jobid: 17 output: out/minimap2/sniffles_calls/sample.vcf log: log/minimap2/sniffles_call/sample.log

RuleException: CalledProcessError in line 48 of /home/esdaile/long_read/nano-snakemake/rules/callers.smk: Command 'source activate /home/esdaile/long_read/nano-snakemake/.snakemake/conda/b827a74e; set -euo pipefail; sniffles --mapped_reads out/minimap2/alignment/sample.bam --vcf out/minimap2/sniffles_calls/sample.vcf --threads 1 2> log/minimap2/sniffles_call/sample.log ' returned non-zero exit status 1. File "/home/esdaile/long_read/nano-snakemake/rules/callers.smk", line 48, in __rule_sniffles_call File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job sniffles_call since they might be corrupted: out/minimap2/sniffles_calls/sample.vcf Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message

[wdecoster]

Is there an error message in log/minimap2/sniffles_call/sample.log?

[EEsdaile]

Hi Wouter, all it says is "Too few reads detected in out/minimap2/alignment/sample.bam".

[wdecoster]

Well, that doesn't look good, let's take a step back and check your alignment. What is returned by samtools idxstats out/minimap2/alignment/sample.bam?

How much data do you have here?

[EEsdaile]

Here is the top of the output: chr1 188260577 0 0
chr10 85155674 0 0
chr11 61676917 0 0
chr12 36992759 0 0
chr13 43784481 0 0
chr14 94600235 0 0
chr15 92851403 0 0
chr16 88962352 0 0
chr17 80722430 0 0
chr18 82641348 0 0

If you start from the bottom there seems to be thousands of unassigned reads.

I have successfully mapped this data with minimap2 before with minimap2 -t 5 -ax map-ont --MD -L . Could I somehow use that previously made file? The only other difference is that I used the original gzipped genome instead of having to gunzip and rezip as a bzip to index for snakemake. (zcat equCab3.fa.gz | bgzip -c > equCab3_bgzip.fa.gz samtools faidx equCab3_bgzip.fa.gz)

[wdecoster]

Well that alignment doesn't look right. You could edit the snakemake code to start from a previous alignment, but that will require that you know snakemake. What is in the log file of the aligment step?

[EEsdaile]

I know the very basics of snakemake. If you can tell me about what to edit in which file I might be able to sort it out. If it's that easy.

/nano-snakemake/log/minimap2/sample.log is a blank file.