Make.contigs name mismatch in forward and reverse fastq files

mothur bugs
1

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

2

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

3

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

4

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

Thanks,
Pat

5

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

6

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