Hello! I've recently started working with NGS data and I got stuck and was wondering if anyone could help me. Before I started I used some sequencing data from a colleague of mine to get my pipeline up and running and so far that works.
What I am doing is the following:
Create index files of hg19 using BWA index
Use BWA mem to align my fastq.gz files
Use Samtools to create BAM files
Use lofreq to call the variants
This all works completely fine using the genomic data from my colleague but my approach was a little different. I sequenced cDNA and I was wondering if I could use a fasta file created by myself of the gene of interest which I downloaded from UCSC. When I try to create index files from that fasta using BWA index, it does so very rapidly (the cDNA is only 700bp), but afterwards it gives me Segmentation fault (core dumped). I think this has to do with my custom fasta and accompanying index files. Any thoughts?
Thanks in advance!
The custom fasta I want to use:
> [HPRT cDNA NGS full sequence.xdna] - 1289 bp TTACCTCACTGCTTTCCGGAGCGGTAGCACCTCCTCCGCCGGCTTCCTCCTCAGACCGCTTTTTGCCGCGAGCCGACCGG TCCCGTCATGCCGACCCGCAGTCCCAGCGTCGTGATTAGCGATGATGAACCAGGTTATGACCTAGATTTGTTTTGTATAC CTAATCATTATGCCGAGGATTTGGAAAAAGTGTTTATTCCTCATGGACTGATTATGGACAGGACTGAAAGACTTGCTCGA GATGTCATGAAGGAGATGGGAGGCCATCACATTGTGGCCCTCTGTGTGCTCAAGGGGGGCTATAAGTTCTTTGCTGACCT GCTGGATTACATTAAAGCACTGAATAGAAATAGTGATAGATCCATTCCTATGACTGTAGATTTTATCAGACTGAAGAGCT ACTGTAATGATCAGTCAACGGGGGACATAAAAGTTATTGGTGGAGATGATCTCTCAACTTTAACTGGAAAGAATGTCTTG ATTGTTGAAGATATAATTGACACTGGTAAAACAATGCAAACTTTGCTTTCCCTGGTTAAGCAGTACAGCCCCAAAATGGT TAAGGTTGCAAGCTTGCTGGTGAAAAGGACCTCTCGAAGTGTTGGATACAGGCCAGACTTTGTTGGATTTGAAATTCCAG ACAAGTTTGTTGTTGGATATGCCCTTGACTATAATGAGTACTTCAGGGATTTGAATCACGTTTGTGTCATTAGTGAAACT GGAAAAGCCAAATACAAAGCCTAAGATGAGCGCAAGTTGAATCTGCAAATACGAGGAGTCCTGTTGATGTTGCCAGTAAA ATTAGCAGGTGTTCTAGTCCTGTGGCCATCTGCCTAGTAAAGCTTTTTGCATGAACCTTCTATGAATGTTACTGTTTTAT TTTTAGAAATGTCAGTTGCTGCGTCCCCAGACTTTTGATTTGCACTATGAGCCTATAGGCCAGCCTACCCTCTGGTAGAT TGTCGCTTATCTTGTAAGAAAAACAAATCTCTTAAATTACCACTTTTAAATAATAATACTGAGATTGTATCTGTAAGAAG GATTTAAAGAGAAGCTATATTAGTTTTTTAATTGGTATTTTAATTTTTATATATTCAGGAGAGAAAGATGTGATTGATAT TGTTAATTTAGACGAGTCTGAAGCTCTCGATTTCCTATCAGTAACAGCATCTAAGAGGTTTTGCTCAGTGGAATAAACAT GTTTCAGCAGTGTTGGCTGTATTTTCCCACTTTCAGTAAATCGTTGTCAACAGTTCCTTTTAAATGCAAATAAATAAATT CTAAAAATT
bwa index fastafile.fa bwa mem fastafile.fa sample1Fw.fastq.gz sample1Rv.fastq.gz > sample1.sam The error: [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 66226 sequences (10000126 bp)... ./bwascript-test.sh: line 2: 26915 Segmentation fault (core dumped)
line 2 is the bwa mem I typed above.