# make.contigs multiple warnings

**URL:** <https://forum.mothur.org/t/make-contigs-multiple-warnings/1570>\
**Category:** Commands in mothur\
**Created:** [November 5, 2013, 9:54am UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570 "2013-11-05T09:54:41Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![dackfc](https://avatars.discourse-cdn.com/v4/letter/d/848f3c/32.png) [@dackfc](https://forum.mothur.org/u/dackfc)\
**Post date:** [November 5, 2013, 9:54am UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/1 "2013-11-05T09:54:41Z")

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We have previously followed the Mothur SOP for wet lab and MiSeq SOP for processing / analysis. This worked very last last time. However, in a recent run of 192 samples the make.contigs commands is throwing back numerous warnings. Once the make.contigs command is initiated it runs seemingly fine for about 10 minutes then the following appears…

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40000  
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[WARNING]: reading CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACG expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read M01

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<div class="post-metadata">

**Author:** ![dackfc](https://avatars.discourse-cdn.com/v4/letter/d/848f3c/32.png) [@dackfc](https://forum.mothur.org/u/dackfc)\
**Post date:** [November 5, 2013, 9:56am UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/2 "2013-11-05T09:56:15Z")

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FHHHHHHHHHHHGHHGGEEGHHBHHGGGFGDH########?#################\<??FFGHHFHHHHGHGHH##.###\>\>############.\<;:.:####;=:###9;.#.;;A9#########;;;:;BFD;@EEEFFAAAFF.;:[9BFFF9-9BFAF-@DE.ABBFF9BF](mailto:9BFFF9-9BFAF-@DE.ABBFF9BF). for fasta and CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACG for quality, ignoring.[WARNING]: Lengths do not match for sequence M01

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<div class="post-metadata">

**Author:** ![dackfc](https://avatars.discourse-cdn.com/v4/letter/d/848f3c/32.png) [@dackfc](https://forum.mothur.org/u/dackfc)\
**Post date:** [November 5, 2013, 9:57am UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/3 "2013-11-05T09:57:42Z")

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For some reason I cannot paste the whole list of issues. I have log files and will be happy to attach (if possible) or email. Let me know.

Thanks advance,  
Chris

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**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:** [November 6, 2013, 5:36pm UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/4 "2013-11-06T17:36:53Z")

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Looks like an error in the fastq file. Can you use grep to see if there is indeed some sort issue with the input file?

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<div class="post-metadata">

**Author:** ![dackfc](https://avatars.discourse-cdn.com/v4/letter/d/848f3c/32.png) [@dackfc](https://forum.mothur.org/u/dackfc)\
**Post date:** [November 6, 2013, 9:30pm UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/5 "2013-11-06T21:30:49Z")

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Thanks for the response. I will do this ASAP. To confirm, to use grep on a MAC I will open the terminal and cd the folder with the fastq files and run ‘grep -c “\>” \*.fastq’?

Thanks,  
Chris

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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:** [November 8, 2013, 3:31pm UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/6 "2013-11-08T15:31:09Z")

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grep -C 50 “STRINGTOMATCH” filename You probably want a longer string than \> to avoid alot of grep matches.

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<div class="post-metadata">

**Author:** ![dackfc](https://avatars.discourse-cdn.com/v4/letter/d/848f3c/32.png) [@dackfc](https://forum.mothur.org/u/dackfc)\
**Post date:** [November 17, 2013, 12:18pm UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/7 "2013-11-17T12:18:26Z")

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Thank you! We identified 10 fastq files which were causing the issue. Removing these files from stability.files allowing the make.contigs command to run with no errors.

Any ideas on what was causing the issue? There is nothing striking about files that were corrupt that jumps out and this has never happened before…

Thanks,  
Chris

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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:** [November 18, 2013, 11:29am UTC](https://forum.mothur.org/t/make-contigs-multiple-warnings/1570/8 "2013-11-18T11:29:04Z")

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It may not be the entire file. Perhaps just part of the file just corrupted? Hard to say why. You could ask for another copy from your provider.