Make.contigs name mismatch in forward and reverse fastq files

Hi,

I have been trying to run mother v 1.44.1 and mothur v 1.48.0 on a set of 16S fast files. I am seeing the follow error for a fair number of my reads:

[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, (read in question).

I am using the command:

make.contigs(file=IDtestStudy.txt, trimoverlap=F, processors=8)

When I look into my fast files a bit further, it appears there isn’t actually a mismatch in the read names. For example:

[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, MS5_46448_1_2113_21855_8079/1.

When I grep the relevant read names in my forward and reverse files, I successfully can see them:

$ grep MS5_46448:1:2113:21855:8079/1 46448_2F.fastq
@MS5_46448:1:2113:21855:8079/1

$ grep MS5_46448:1:2113:21855:8079/2 46448_2R.fastq
@MS5_46448:1:2113:21855:8079/2

Apologies if I’m missing something obvious but for some files this is removing a large number of reads from my mothur run.

Best wishes,
Dinesh

Hi Dinesh -

Can you run the grep commands using the -B 12 flag? This will show the 12 lines before your sequence name. I wonder if there’s something before your sequence that’s missing and throwing things out of sync.

Thanks,
Pat

Hi Pat,

Thanks very much for getting back and your help with this. As requested, here is the output with the additional lines from the fastq files:

$ grep MS5_46448:1:2113:21855:8079/1 -B 12 46448_2F.fastq

@MS5_46448:1:1104:23350:13510/1

ATAGAGCGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCTCTTCGGAGGTACTCGAGTGGCGAACGGGTGAGTAACACGTGGGTGATCTGCCCTGCACTCTGGGATAAGCCTGGGAAACTGGGTCTAATACCGGATAGGACCATGCTTTAGTGTGTGTGGTGGAAAGTTTTTTCGGTGTAGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCGGCGACGGGTAGCCGGACTGAGAGGTTGGTCGGG

CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEEFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGCEGGGGGGFFGGFFGGGGGGGGGF*A8CGFFDGGGGGGGGGGGGGFGG@FFFFFFDCDDDFF?FF>FFGBBFGEFG3DFF:AAFGGF<C:BCFF:9B60(7;0<7<>?<9656>BFB4>FF?(7:<>D)

@MS5_46448:1:1102:12104:9479/1

TTTTAGAGTTCGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGAAGTTAGGAAGCTTGCTTCTGATACTTAGTGGCGGACGGGTGAGTAATGCTTAGGAATCTGCCTAGTAGTGGGGGATAACTTGGGGAAACCCAAGCTAATACCGCATACGACCTACGGGTGAAAGGGGGCTTTTAGCTCTCGCTAATAGATGAGCCTAAGTCGGATTAGCTGGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCA

CCCCCGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGFGGFFFFFFFFGFFFFFFFGFFFF?>>GFG:5C6FF:FFFFFFFFGGFFF;>?FFFFFGFFF<BB:26<BF:?FF<ADFFF0

@MS5_46448:1:1113:18673:6112/1

TCTTAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCTTAACACATGCAAGTCGAACGAAGTTAGGAAGCTTGCTTCTGATACTTAGTGGCGGACGGGTGAGTAATGCTTAGGAATCTGCCTAGTAGTGGGGGATAACTTGGGGAAACCCAAGCTAATACCGCATACGACCTACGGGTGACAGGGGGCTTTTAGCTCTCGCTATTAGATGAGCCTAAGTCGGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCC

CCCCCGAGGGGGGGGFGGGGGGGGFFGGGGGGGGGGGGGGGGGGDGGGFGGGGGGGGGGGGGGGGGEEGGGGGGGGGGFGDGFFGGGFEFFGFFGGGGGGGGGGGEFDABGFFFFGF,C<FFFEEGGGGGGE=FFFEGG:BFFFFDGFD8C:CDFFGGF,CFGGCFAGEGEEGG>EEEGGFEGGGEG,>CCCEGGGGFCFGG7;FCEGGGGG?GGGF+6?F?FFFFFG3B5BF?FG??=DF@F:7CF9F7066C48CF:GGF;F6>(:?<BBCF<4??9B>(87,.6A))44(

@MS5_46448:1:2113:21855:8079/1

$ grep MS5_46448:1:2113:21855:8079/2 -B 12 46448_2R.fastq

@MS5_46448:1:1106:20741:13533/2

TCGCGCTGCCACCCACCCGCCTCCCCCCCCCCCACCACCACCCCCGCGCCACCCCCCCCCCCCCACCCCCCCCCCCCACCCCCCCCCCCCACCCCCCCCCCCCACCCCCGCCCACCACCCCCCCACCGCCACCCCCCCCCCCCCCCACCCACCCCCCCCCCCCCCCTCCCCACCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCACACCCCCACCCCCCCCCCCACCCCGCCCCCACCCACCCCCCCCTCACCCCCCGCCCACCACACCCCCACCACCACCCCCCCCAACACACC

-6,=++C,;-C,B,+8+,8EF@+@++++6++84,@,9C?@++4++84BF+6+C7:CE88B+38>>F*>43=1CCCCC>:18/28:C88888C211;12**/:1:.0*):5C8*/)1/2:CD*/955C5CC1:52))2/:).93<>G8=758).5):3(>4(7894)7*1;D:D/(:6(4(70/1((4((((4>7(4(41>0>?B?:,)(0((((-(.2;(-((,)1(2314((20(1(41((4,4,(9>1>6((-(,(44

@MS5_46448:1:1102:12104:9479/2

TTTTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCAGACCAGCTACAGATCGTCGCCTTGGTAGGCCTTTACCCCACCAACCAGCTAATCCGACTTAGGCTCCTCTCTTCTCACGAACAACCCCCCCCCCCCACCCCCCCCCTCCCACCCCCCACCCGCCACCCTCTCCCCCCCCCTCCCCCCCCCCCTCTCCACCCCCCCCTCCCACCCCCCCCCCTACCCCCCACCCACCCCCCCCCCACCCCCCCCCACCCCCCACCCCACCCCCCACC

CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGG,9)0+=,@,69,++4+,68=+C89=>C;);@5>@D?38)/(0)()((())/)0),(…**).06,-5/7)(11:800,9)(:(-13?AE),24(3404*.(.()-4;1567((4>:0(3(-,(4((,((8(39(,4609:329(4,((32(,(,(-2(4(2(-4

@MS5_46448:1:1113:18673:6112/2

GGGTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCAGACCAGCTACAGATCGTCGCCTTGGTAGGCCTTTACCCCACCAACTAGCTAATCCGACTTAGGCTCATCTAATAGCGAGAGCTAAAAGCCCCCTTTCACCCGTAGGTCGTATCCCCCCCCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBFGGGFGGGGGGGGGGGEGGGGGGGG;CFFGFFGFEFGGGGGGGGGEEGGGGGGGGGFGFGGFDEGGGGGFFGGFGGGGGECFEGDGGGDFGFGGGGGFGFGGCFEGAFGFCFGGGGGGFCF8DF6D@ED6DFDBFF:C5+0?)***:5)…1711:EGBF>EC<17CEFBGBFD9G166299ED039B0(46GG991C3B69>F69>FFFFFFB>B;GGFFF(3BBFFBFFFFFFFBFFFBFFFBFFFFBB>BF29>BFF

@MS5_46448:1:2113:21855:8079/2

Best wishes,
Dinesh

Hmmm. Can you send the two files to mothur.bugs@gmail.com?

Thanks,
Pat

Thanks Pat, you should have these now on the email stated. Please let me know if they’re not with you - the folder is zipped but still very large!

Bw
Dinesh

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.