zipped input files

[CosteaPaul]

This should support fastq.gz input files :).

[AlessioMilanese]

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

[CosteaPaul]

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:

• similarity to the reference gene (>97%), and

• 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...

[CosteaPaul]

Never mind. This was on me. Seems my gpfs takes a while to sync properly.

I owe you a beer for jumping the gun :).

[AlessioMilanese]

Sounds good 🍺 :)