Closed CosteaPaul closed 1 year ago
mOTUs supports fastq.gz files. From the manual:
Input options:
-f FILE[,FILE] input file(s) for reads in forward orientation, fastq(.gz)-formatted
-r FILE[,FILE] input file(s) for reads in reverse orientation, fastq(.gz)-formatted
-s FILE[,FILE] input file(s) for unpaired reads, fastq(.gz)-formatted
On the latest version:
motus profile -s someFile_S1_L001_R1_001.fastq.gz
2023-02-17 14:49:09 Map reads to the marker gene database Reads are aligned (by BWA) to marker gene sequences in the reference database Reads are filtered for:
length of the alignment (at least 75 nucleotides, -l option)
Number of detected lanes: 1
2023-02-17 14:49:09 Run bwa on lane 1
Error: file someFile_S1_L001_R1_001.fastq.gz is not a fastq file
Unzipping and running works fine...
Never mind. This was on me. Seems my gpfs takes a while to sync properly.
I owe you a beer for jumping the gun :).
Sounds good 🍺 :)
This should support fastq.gz input files :).