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Old 11-06-2011, 05:53 AM   #1
Location: Scandinavia

Join Date: Dec 2009
Posts: 20
Question Unmatched read name error when converting csfasta to fastq with

I'm encountered with "unmatched read name" error when I converting paired SOLiD csfasta files to fastq by using from bwa-0.5.9

The error message:
** unmatched read name: '>4_26_52_F3
' != '>4_26_52_F3

I read there was suggestion to modify the script as mentioned by

1. drio's post in PE SOLiD reads alignment by bwa thread.

2. javijevi's post in bwa samse segmentation fault thread.

I tired the modification and the "unmatched read name" error remained.

Could anyone shares your solution for this?

Thank you very much.
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Old 11-06-2011, 07:48 AM   #2
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 700

It's dieing in this routine:
sub read1 {
  my $i = shift(@_);
  my $j = ($i-1)<<1;
  my ($key, $seq);
  my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
  while (<$fhs>) {
        my $t = <$fhq>;
        if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
          $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
          die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t);
          my $name = "$pre:$1_$2_$3/$i";
          $_ = substr(<$fhs>, 2);
          my $s = $_;
          $_ = <$fhq>;
          $seq = qq/\@$name\n$s+\n$_\n/;
  return defined($seq)? ($key, $seq) : ();
Things you might try are modifying this to print out $t and the line number. Please do it on a copy of so you keep the original. You can look at that line number in both files to see what's up. I'm not really sure what's up with that extra carriage return(s) in the error message.

Last edited by Richard Finney; 11-06-2011 at 07:51 AM. Reason: format
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Old 11-06-2011, 08:18 PM   #3
Location: Scandinavia

Join Date: Dec 2009
Posts: 20

Thanks Richard Finney.

I came across to this piece of modified script by bgulko in bwa color-space index thread.

I did minor changed as suggested by drio's post in PE SOLiD reads alignment by bwa thread for pairend reads on this modified script.

Without that minor changed on that script, it only converted the F3 csfasta to single end reads fastq.

So far, the script worked with no complaint. I got read1.fastq and read2.fastq after the converting task done. However, I'm not yet carry out the mapping task. I will do it later.
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bwa, csfasta, fastq, solid, solid2fastq

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