# Make Contigs - name mismatch problem

**URL:** <https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151>\
**Category:** mothur bugs\
**Created:** [October 5, 2021, 11:11pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151 "2021-10-05T23:11:23Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![JerryC](https://avatars.discourse-cdn.com/v4/letter/j/3e96dc/32.png) [@JerryC](https://forum.mothur.org/u/JerryC)\
**Post date:** [October 5, 2021, 11:11pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/1 "2021-10-05T23:11:24Z")

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Newbie here …

Mothur version 1.45.3  
Windows 11, i9 + 64GB RAM  
MiSeq Illumina fungal ITS data  
No pre-processing of the supplied gz files.  
Forward/reverse files contain equal numbers of entries.

Commands used …  
**make.file(inputdir=., type=gz, prefix=stability)**  
**make.contigs(file=stability.files, processors=15)**

I get lots of warnings and lose about half the reads.  
e.g.  
`>>>>> Processing file pair D:\Docs\MothurData\eDNA\testmake\lepidium __SV_DOC_-LK-04_6__ ITS3_KYO2_R1.fastq.gz - D:\Docs\MothurData\eDNA\testmake\lepidium __SV_DOC_-LK-04_6__ ITS3_KYO2_R2.fastq.gz (files 1 of 1) <<<<<`

gives …  
**[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M07073\_33\_000000000-JKRRG\_1\_1107\_9781\_22902\_\_lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2.**

But here is the entry in the R1 file …  
**@M07073:33:000000000\_JKRRG:1:1107:9781:22902\_\_lepidium\_\_SV\_DOC\_\_LK\_04\_6\_\_ITS3\_KYO2**  
ATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGCGTCACAAATCGTCGTCCCACTCACGAAATTTTGCGAGTGCGGGACGGAAGCTGGTCTCCCGTGTGTTACCGCACGCGGTTGGCCAAAATCTGAGCTGAGGATGCTGGGAGCGTCCCGACATGCGGTGGTGATCTAAAAGCCTCTTCATATTGCCGGTCGCTCCTGTCCGTAAGCTCTCG  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCEGGGGGGGGFGGGGFGGGGGFGFFGFFF;\>?FFFFF?F?FF:6?AFFF(

and here is the entry in the R2 file …

**@M07073:33:000000000\_JKRRG:1:1107:9781:22902\_\_lepidium\_\_SV\_DOC\_\_LK\_04\_6\_\_ITS3\_KYO2**  
TTAAACTCAGCGGGTGATCCCGCCTGACCTGGGGTCGCTTTGAGGACATTGGGTCAACGAGAGCTTACGGACAGGAGCGACCGGCAATATGAAGAGGCTTTTAGATCACCACCGCATGTCGGGACGCTCCCAGCATCCTCAGCTCAGATTTTGGCCAACCGCGTGCGGTAACACACGGGAGACCAGCTTCCGTCCCGCACTCGCAAAATTTCGTGAGTGGGACGACGATTTGTGACGCCCAGGCAGACGTGCCCTCGGCCAGAAGGCTTGGTGCGC  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGB\<FGFFFFFFE?99;\>F??\>DDGGFFFFGGGF8FGGF?F\>9\>E3CFFAB75\>\>BF9\<B:B\<:610441\<?B\<(4:\<3627446?:68.491,

The names are the same.

I tried processing the uncompressed files, running on 1 processor, changing all dashes in filenames/sequence labels to underscores. I get the same warnings and dropped contigs.

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 8, 2021, 12:32pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/2 "2021-10-08T12:32:33Z")

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Could you send the D:\Docs\MothurData\eDNA\testmake\lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2\_R1.fastq.gz and D:\Docs\MothurData\eDNA\testmake\lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2\_R2.fastq.gz files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) so I can troubleshoot the issue for you?

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 12, 2021, 2:16pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/3 "2021-10-12T14:16:27Z")

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Thanks for sending your files. The make.comtigs command expects the forward reads to be in the same order as the reverse reads in the fastq files. The “missing” reads are present in the files, but the order is swapped. For example:

R1 file order  
@M07073:33:000000000-JKRRG:1:2106: **27076** :10535\_\_lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2  
TTAAACTCAGCGGGTGATCCCGCCTGACCTGGGGTCGCTTTGAGGACAT…  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG…  
@M07073:33:000000000-JKRRG:1:2106: **27054** :10535\_\_lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2  
TTAAACTCAGCGGGTGATCCCGCCTGACCTGGGGTCGCTTTGAGG…  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGG…

R2 file order  
@M07073:33:000000000-JKRRG:1:2106: **27054** :10535\_\_lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2  
TTAAACTCAGCGGGTGATCCCGCCTGACCTGGGGTCGCTTTGAGG…  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGG…  
@M07073:33:000000000-JKRRG:1:2106: **27076** :10535\_\_lepidium\_\_SV\_DOC\_-LK-04\_6\_\_ITS3\_KYO2  
TTAAACTCAGCGGGTGATCCCGCCTGACCTGGGGTCGCTTTGAGGACAT…  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG…

The mismatch caused the command to skip 6 reads out of 31320 sequences. I recommend ignoring the warnings and proceeding with the analysis.

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<div class="post-metadata">

**Author:** ![JerryC](https://avatars.discourse-cdn.com/v4/letter/j/3e96dc/32.png) [@JerryC](https://forum.mothur.org/u/JerryC)\
**Post date:** [October 16, 2021, 7:25am UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/4 "2021-10-16T07:25:28Z")

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Hi Sarah,

I just wondered if you’d had a chance to test the files – whether the issue is with my platform, the data files, or the code.

Thanks,

Jerry

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [October 19, 2021, 3:46pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/5 "2021-10-19T15:46:31Z")

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Hi Jerry,

Yes, I was able to find the issue. In my post above, I explained the issue is caused by the data files. The make.contigs command expects the forward reads to be in the same order as the reverse reads in the fastq files. The “missing” reads are present in the files, but the order is swapped. The mismatch caused the command to skip 6 reads out of 31320 sequences. I recommend ignoring the warnings and proceeding with the analysis.

Kindly,  
Sarah

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<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [October 29, 2021, 3:46pm UTC](https://forum.mothur.org/t/make-contigs-name-mismatch-problem/21151/6 "2021-10-29T15:46:58Z")

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