I have a draft, Illumina-based, genome and bunch of reseq samples. I generated bam files using
bowtie2 and marked duplicates using
Now, when I tried to call SNPs using freebayes, I got cryptic
Segmentation fault (core dumped) even when I tried to run it in verbose debugging mode (
-dd). Do you have an idea where might be a problem?
freebayes -f data/Afus1/genome.fa -b reseq1.sorted.rmdup.bam reseq2.sorted.rmdup.bam -dd loading fasta reference data/Afus1/genome.fa Opening 2 BAM format alignment input files done Number of ref seqs: 821466 Number of target regions: 0 no sample list file given, reading sample names from bam file found 2 samples in BAM file Segmentation fault (core dumped) ```