Hi,
I am having a problem using cmpfastq, even if I've been using it reliably for months.
Normally, I can grab my trimmed 1_1.fastq and 1_2.fastq, process it through cmpfastq, and get out my .common.out and .unique.out files for downstream processes. However, a couple data sets are really giving my trouble... the cmpfastq spits out all error messages for every line of .fastq and fails to generate the appropriate files.
Here is a sample of the output data:
BEGIN cmpfastq3 on TpruniS3_1.trimmed TpruniS3_2.trimmed at Wed Oct 10 15:00:08 EDT 2012
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:17085:1532/2
Could not match the sequence ID from the name: TACTCCTACTGCGCAGCAATATTATTCTTTCGTTAGAGCTAAAAGGCAGAGTGGGAATCGAACCCACTTCGTTAGATTTGCAATC
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 555??BBDDDDDDBDCCFFFFEFI;BEFHIIHFHFHH@@GHHIFHHHFEFH8CD@@BFD@EFHCEEHECFFHIIFHHDFGHIIHH
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:16787:1535/2
Could not match the sequence ID from the name: TAGACGTTTAAGTGACACCGAAAGAAGAAAGAGCTTTGTAGATGCTTAGCGCGGTCTACGAGCCTGGCGGATCAGAAAGCGGAAG
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 5<?????DDDDDBDBFFFFFFHDACFHFHHB=CFDGHHHEDGGFGFGGHIHHC>EDEHHHHHHHB@?DHHCHHFFHHD=F;A@EE
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:14795:1537/2
Could not match the sequence ID from the name: AACGGAGCGAAGGATTTTAGCTTCACGAATTTCCCAAACTTGGCGAGGTCCTGTGTCGATTCCCGGACTTCCTTGGTCTTTGCGCC
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 5<????@DDDDBDDBFFFFFFIIIHIIHHEHIHIIIFHHH/AFFCH++?EE?EFGGHHFF-CA-5CEEAGH,CCDF@DBGDFFCEE
Does anyone have an idea?
Thanks for the help!
I am having a problem using cmpfastq, even if I've been using it reliably for months.
Normally, I can grab my trimmed 1_1.fastq and 1_2.fastq, process it through cmpfastq, and get out my .common.out and .unique.out files for downstream processes. However, a couple data sets are really giving my trouble... the cmpfastq spits out all error messages for every line of .fastq and fails to generate the appropriate files.
Here is a sample of the output data:
BEGIN cmpfastq3 on TpruniS3_1.trimmed TpruniS3_2.trimmed at Wed Oct 10 15:00:08 EDT 2012
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:17085:1532/2
Could not match the sequence ID from the name: TACTCCTACTGCGCAGCAATATTATTCTTTCGTTAGAGCTAAAAGGCAGAGTGGGAATCGAACCCACTTCGTTAGATTTGCAATC
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 555??BBDDDDDDBDCCFFFFEFI;BEFHIIHFHFHH@@GHHIFHHHFEFH8CD@@BFD@EFHCEEHECFFHIIFHHDFGHIIHH
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:16787:1535/2
Could not match the sequence ID from the name: TAGACGTTTAAGTGACACCGAAAGAAGAAAGAGCTTTGTAGATGCTTAGCGCGGTCTACGAGCCTGGCGGATCAGAAAGCGGAAG
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 5<?????DDDDDBDBFFFFFFHDACFHFHHB=CFDGHHHEDGGFGFGGHIHHC>EDEHHHHHHHB@?DHHCHHFFHHD=F;A@EE
Could not match the sequence ID from the name: @M00649:2:000000000-A1721:1:1101:14795:1537/2
Could not match the sequence ID from the name: AACGGAGCGAAGGATTTTAGCTTCACGAATTTCCCAAACTTGGCGAGGTCCTGTGTCGATTCCCGGACTTCCTTGGTCTTTGCGCC
Could not match the sequence ID from the name: +
Could not match the sequence ID from the name: 5<????@DDDDBDDBFFFFFFIIIHIIHHEHIHIIIFHHH/AFFCH++?EE?EFGGHHFF-CA-5CEEAGH,CCDF@DBGDFFCEE
Does anyone have an idea?
Thanks for the help!
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