Segmentation fault (core dumped)

Dear Fritz,

I’m running ngmlr and sniffles to find small insertions in prokaryotic genomes. Although the strategy worked for every chromosome I have tried, just half of my samples (3/6) could be processed when I input small regions of interest (~50kbp) extracted from plasmids. You can find the program calls and additional info below.

• 24 threads

• ngmlr call:

ngmlr -t $threads -r ${inputdir}/${i}_polished.fa \
          -q ${fastqdir}/${i}.fastq.gz -o ${samdir}/${i}.sam \
          --no-smallinv \
          --bam-fix \
          -x ont > ${samdir}/${i}_ngmlr.log 2> ${samdir}/${i}_ngmlr.err

• converting and sorting SAM to BAM using samtools 1.9 (also tried with 1.7)

• sniffles call:

sniffles -t $threads \
            -m ${bamdir}/${i}.bam \
            --min_support 1 \
            --max_distance 500 \
            --max_num_splits 2 \
            --min_length 100 \
            --num_reads_report 5 \
            --min_seq_size 1000 \
            --report_seq \
            -v ${vcfsniffles}/${i}.vcf > ${vcfsniffles}/${i}_sniffles.log 2> ${vcfsniffles}/${i}_sniffles.log

• sniffles stdout and stderr:

Estimating parameter...
	Max dist between aln events: 4
	Max diff in window: 50
	Min score ratio: 2
	Avg DEL ratio: 0.0576036
	Avg INS ratio: 0.124236
Start parsing... barcode01_gvp
Finalizing  ..
Segmentation fault (core dumped)

For the failed samples, the output vcf file is empty.

I have tried to run it in two machines, and the error is reproducible in both of them. Could you please take a look at this issue? I’m privately sharing the files with you by e-mail.

Best regards, Alan.

[fritzsedlazeck]

Dear Alan, Thanks for reporting this. I will have a look. You might want to check min support = 2 in the mean time . Cheers Fritz

[fritzsedlazeck]

We just pushed a completely new version of Sniffles (v2.0.0.2) and hope this will be resolved.