Fasta Format And Maq

Question

[joaslucas]

I am trying to use the genome of Mycobacterium tuberculosis as a ref seq but it seems that maq is not recognizing it as fasta format. I am using the following command line:

maq.pl easyrun outdir MTBH37RV.fasta B4_GCCAT_L002_R1_001.fastq

and it is returning: "Cannot guess the format of file '/home/Documentos/maq-0.7.1/MTBH37RV.fasta'. at /usr/local/bin/maq.pl line 107."

Can someone give a help?

Thanks

Answer 1

[fo3c]

It seems that you are missing a -d in there.

See their example: maq.pl easyrun -d outdir ref.fasta reads.fastq

[joaslucas]

Thanks got it, I was reaaly missing the -d.