Comments (3)
Hello,
I was able to reproduce your problem
$ bsmapz -a SRR6328781_1.fastq -b SRR6328781_2.fastq -d WCG_genome_v2.fa -o SRR6328781.bam -p 64 -A AGATCGGAAGAGC -w 100 -r 0 -q 10
[bsmapz] @Wed Aug 5 15:11:59 2020 loading reference file: WCG_genome_v2.fa (format: FASTA)
Segmentation fault
and solved it by splitting reference sequence into lines of 70 characters with FASTA-formatter.
$ fasta_formatter -i WCG_genome_v2.fa -o WCG_genome_v2_70w.fa -w 70
$ ./bsmapz -a SRR6328781_1.fastq -b SRR6328781_2.fastq -d WCG_genome_v2_70w.fa -o SRR6328781.bam -p 64 -A AGATCGGAAGAGC -w 100 -r 0 -q 10
[bsmapz] @Wed Aug 5 15:14:40 2020 loading reference file: WCG_genome_v2_70w.fa (format: FASTA)
[bsmapz] @Wed Aug 5 15:14:57 2020 12 reference seqs loaded, total size 404611775 bp. 17 secs passed
[bsmapz] @Wed Aug 5 15:15:11 2020 create seed table. 31 secs passed
[bsmapz] @Wed Aug 5 15:15:11 2020 Pair-end alignment(64 threads),
Input read file #1: SRR6328781_1.fastq (format: FASTQ)
Input read file #2: SRR6328781_2.fastq (format: FASTQ)
Output file: SRR6328781.bam (format: SAM, automatically convert to BAM)
You can use another width besides 70, BSMAPz just can't handle the whole chromosome on a single line.
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Hi,I am meeting with the same problem, have you resolve it?
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Hello,
I was able to reproduce your problem
$ bsmapz -a SRR6328781_1.fastq -b SRR6328781_2.fastq -d WCG_genome_v2.fa -o SRR6328781.bam -p 64 -A AGATCGGAAGAGC -w 100 -r 0 -q 10 [bsmapz] @Wed Aug 5 15:11:59 2020 loading reference file: WCG_genome_v2.fa (format: FASTA) Segmentation fault
and solved it by splitting reference sequence into lines of 70 characters with FASTA-formatter.
$ fasta_formatter -i WCG_genome_v2.fa -o WCG_genome_v2_70w.fa -w 70 $ ./bsmapz -a SRR6328781_1.fastq -b SRR6328781_2.fastq -d WCG_genome_v2_70w.fa -o SRR6328781.bam -p 64 -A AGATCGGAAGAGC -w 100 -r 0 -q 10 [bsmapz] @Wed Aug 5 15:14:40 2020 loading reference file: WCG_genome_v2_70w.fa (format: FASTA) [bsmapz] @Wed Aug 5 15:14:57 2020 12 reference seqs loaded, total size 404611775 bp. 17 secs passed [bsmapz] @Wed Aug 5 15:15:11 2020 create seed table. 31 secs passed [bsmapz] @Wed Aug 5 15:15:11 2020 Pair-end alignment(64 threads), Input read file #1: SRR6328781_1.fastq (format: FASTQ) Input read file #2: SRR6328781_2.fastq (format: FASTQ) Output file: SRR6328781.bam (format: SAM, automatically convert to BAM)
You can use another width besides 70, BSMAPz just can't handle the whole chromosome on a single line.
Good, I've got it. Thank a lot!
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