Hi, I downloaded mothur v.1.37.0 today and had issues with running make.contigs with a stability file when my files were in .gz format. However, when I decompressed the files and changed the names in the stability file accordingly to .fastq instead of .gz, everything seems to be working just fine.
Not sure if this is helpful, but here are some lines from mothur’s logfile for when the files were in .gz format:
mothur > make.contigs(file=stability.file.small)
Using 1 processors.
Processing file pair 1_R1_001.fastq.gz - 1_R2_001.fastq.gz (files 1 of 1) <<<<<
[ERROR]: Could not open 1_R2_001.fastq.gz
[WARNING]: Blank fasta name, ignoring read.
[WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.Making contigs…
[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704_9_000000000-AA2CM_1_1101_15239_1353.
[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704_9_000000000-AA2CM_1_1101_16354_1491.
[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704_9_000000000-AA2CM_1_1101_13888_1599.
[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704_9_000000000-AA2CM_1_1101_18599_1656.
…
and so on for all sequences.
And then when they were decompressed (I changed the file names in stability.file.small accordingly):
mothur > make.contigs(file=stability.file.small)
Using 1 processors.
Processing file pair 1_R1_001.fastq - 1_R2_001.fastq (files 1 of 1) <<<<<
Making contigs…
and it works just fine.