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samtools faidx Segmentation fault
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Easiest way to fix this is to use seqret in emboss. Just convert the fasta file to ncbi style fasta and it automatically fixes the issue.
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Originally posted by baohua100 View Post$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
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Originally posted by maubp View PostJust for anyone interestedhere is the Biopython equivalent:
Code:from Bio import SeqIO SeqIO.convert("inputfilename.fas", "fasta", "outputfilename.fas", "fasta")
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I had the same sort of segmentation fault. There were no blank lines in my file though. It was apparently due to one of my sequences being >65535 bp (though I don't know why that should matter).
Maubp's biopython code took care of it nicely. Thanks!
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Ah - blank lines at the end of the file can be easily overlooked.
In principle I believe that faidx can cope with blank lines *between* records, but I haven't made time to work out the required code changes to do this. It would probably save some general aggravation though
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Originally posted by jdjax View PostHello, I am coming across the same error. However I have tried that Bio script posted above and it did not work stating some error.
I then looked at my fasta file in vim and it does not have any blank lines in the file.
Does any one have a suggestion of how to fix this problem so that I can use samtools faidx common on my fasta file?
Thank you in advance for your help.
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Originally posted by michmich View PostThe problem is that your FASTA file has a blank lines in it.
you need to get rid of them!!!
you can :g/^$/d in vi/vim editor.
I then looked at my fasta file in vim and it does not have any blank lines in the file.
Does any one have a suggestion of how to fix this problem so that I can use samtools faidx common on my fasta file?
Thank you in advance for your help.
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The problem is that your FASTA file has a blank lines in it.
you need to get rid of them!!!
you can :g/^$/d in vi/vim editor.
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Hello, I have the same problem. I found the last lines in fa file likes:
Code:ggttagggtgtggtgtgtgggtgtgtgtgggtgtggtgtgtgtgggtgtg gtgtgtgggtgtgggtgtgggtgtgggtgtgtgggtgtggtgtgtgggtg tggT
My question is that can I manually modify instead of using a software.
I don't want to install too many software because of rare usage.
Thanks.
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I faced the same problem, but solved with webbrewer's code!
Originally posted by webbrewer View PostThis bioperl snippet fixes the fasta:
Code:use Bio::SeqIO; $in = Bio::SeqIO->new(-file => "inputfilename", -format => 'Fasta'); $out = Bio::SeqIO->new(-file => ">outputfilename", -format => 'Fasta'); while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
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Originally posted by webbrewer View PostThis bioperl snippet fixes the fastahere is the Biopython equivalent:
Code:from Bio import SeqIO SeqIO.convert("inputfilename.fas", "fasta", "outputfilename.fas", "fasta")
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Thanks very much webbrewer for your bioperl fix, it worked perfectly.
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Originally posted by baohua100 View Post[email protected]:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault
What's the meaning of defferent line length ?
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