# make.contigs error (Could not open fast files)

**URL:** <https://forum.mothur.org/t/make-contigs-error-could-not-open-fast-files/2158>\
**Category:** mothur bugs\
**Created:** [December 5, 2014, 5:51am UTC](https://forum.mothur.org/t/make-contigs-error-could-not-open-fast-files/2158 "2014-12-05T05:51:21Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![marrieta](https://avatars.discourse-cdn.com/v4/letter/m/8e7dd6/32.png) [@marrieta](https://forum.mothur.org/u/marrieta)\
**Post date:** [December 5, 2014, 5:51am UTC](https://forum.mothur.org/t/make-contigs-error-could-not-open-fast-files/2158/1 "2014-12-05T05:51:21Z")

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Hi there,

I am having an issue running make.contigs for a recent HiSeq run. I separated all the fastq files into individual experiments and was able to run all my pipeline without issues for all experiments, except for one. In this one I have a group of 24 fastq files and when I use make.contigs gives me this error:

  
\>\>\>\>\> Processing 1cf1\_a1-TCCGTC-GTGAAA\_1.0ffastatemp (file 1 of 6) \<\<\<\<\< [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a1.V3.fasta [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a2.V3.fasta [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a3.V3.fasta [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c1.V3.fasta [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c2.V3.fasta [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c3.V3.fasta Making contigs... [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a1.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a2.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a3.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c1.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c2.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c3.V3.fasta9655.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a1.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a2.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a3.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c1.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c2.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c3.V3.fasta9656.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a1.V3.fasta9657.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a2.V3.fasta9657.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/a3.V3.fasta9657.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c1.V3.fasta9657.temp [ERROR]: Could not open 1cf1\_a1-TCCGTC-GTGAAA\_1.1cf1/c2.V3.fasta9657.temp

The command starts running OK but at the end it is unable to create the aligned fasta files. Given that I’ve already aligned ~250 samples from this same run I can’t understand what’s going on. Any clues?

As always, Thank you!!

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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:** [December 9, 2014, 4:42pm UTC](https://forum.mothur.org/t/make-contigs-error-could-not-open-fast-files/2158/2 "2014-12-09T16:42:45Z")

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Do your group names include ‘/’? The OS is likely seeing that as a folder change. Try changing that to a ‘\_’.