mirdeep2 mapped reference error

Question

[jomagrax]

Hi everyone!

after succesfully indexed the reference genome with bowti-build and mapped with mapper.pl

mapper.pl /home/superuser/jose/TFG/rawdata/control_1_trimmed.fastq  -e -h -i -j -m -p /home/superuser/CAP-miRSEQ/ref/pig_genome.fa -s pig_control_1_collapsed.fa -t pig_control_1_vs_genome.arf

And now Im trying to run the miRDeep2.pl command

 miRDeep2.pl pig_control_1_collapsed.fa /home/superuser/CAP-miRSEQ/ref/pig_genome.fa pig_control_1_vs_genome.arf /home/superuser/CAP-miRSEQ/ref/mature.ssc.dna.fa none /home/superuser/CAP-miRSEQ/ref/hairpin.ssc.dna.fa -t ssc

But i get this error message

The mapped reference id NC_000845.1 from file pig_control_1_vs_genome.arf is not an id of the genome file /home/superuser/CAP-miRSEQ/ref/pig_genome.fa

Wich doesn't seem to be true acording to

 cat /home/superuser/CAP-miRSEQ/ref/pig_genome.fa | grep  NC_000845.1

NC_000845.1 Sus scrofa mitochondrion, complete genome

Does anyone have any idea? Thanks in advance, Jose

Answer 1

[jomagrax]

The problem was that the genome had blankspaces, wich you can remove with

sed 's/[[:blank:]]//g' genome.fa