hisat2-align exited with value 1

Question

[Ahmed]

I am a beginner with command and bioinformatics I am trying to alignment with HISAT2 for RNA seq so first I install the HISTA2 by bioconda using this command:

 bioconda -c install hisat2 

After that I made index for my reference genome with this command:

 hisat2-build -p 3 Danio_rerio.GRCz11.cdna.all.fa /home/ngs/zebra_fish 

The output my reference genome with this names:

zebra_fish.1
zebra_fish.2
zebra_fish.3
zebra_fish.4
zebra_fish.5
zebra_fish.6
zebra_fish.7
zebra_fish.8

Finally I try to do alignment with this command:

hisat2 -p 4 -x /home/ngs/zebra_fish/ zebra_fish.1 zebra_fish.2 zebra_fish.3 zebra_fish.4 zebra_fish.5 zebra_fish.6 zebra_fish.7 zebra_fish.8 -U SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1.fastq -S SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1_chrl.sam 

I get this error:

 hisat2-align exited with value 1

So, please can anyone help me?

Thanks

Answer 1

[GenoMax]

You only need to use the basename of the index when you specify it. Try

hisat2 -p 4 -x /home/ngs/zebra_fish/zebra_fish -U SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1.fastq -S SRR1048063_Zebrafish_pineal_gland_dark_replica_3_1_chrl.sam

[Ahmed]

thanks man <3 you saved me!!