Having problems doing the Hisat2 alignment

Question

[2385676601]

hi guys i try to use hisat2 aligning the fastq file to the index which i have built before, here is the command line:

/home/wyf/miniconda3/bin/hisat2 -x /home/wyf/Pipeline/RNA-seq/02.hisat/Eriocheir_sinensis -p 8 -1 /homRNA-seq/01.afterqc/good/SRR12616419_2.good.fq.gz  -S /home/wyf/Pipeline/RNA-seq/03.bidui/SRR12616419/SRR12616419.sam

then it went wrong! it be like:

Error: Could not open alignment output file /
Error: Encountered internal HISAT2 exception (#1)
Command: /home/wyf/miniconda3/bin/hisat2-align-s --wrapper basic-0 -x /home/wyf/Pipeline/RNA-seq/02.hi0,106,101,92,59,134,128,120,114,112,107,99,76,70,69,54,50,139,132,124,123,122,121,118,117,108,105,103, -1 /tmp/3529138.inpipe1 -2 /tmp/3529138.inpipe2 
(ERR): hisat2-align exited with value 1

i have searched many websites but i cannot find the answer, now i am reindexing my reference genome, hopefully someone will help me, i will appreciate that!!

Answer 1

[ATpoint]

You must only use -1 and -2 if you have paired-end data. For single-end provide the fastq file with -U. I assume here it chokes on the fact that you use -1 without -2.

/home/wyf/miniconda3/bin/hisat2 -x /home/wyf/Pipeline/RNA-seq/02.hisat/Eriocheir_sinensis -p 8 -U /homRNA-seq/01.afterqc/good/SRR12616419_2.good.fq.gz  -S /home/wyf/Pipeline/RNA-seq/03.bidui/SRR12616419/SRR12616419.sam

Is there a reason you use only R2 of that experiment?