make.contigs error (Could not open fast files)

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!!

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