Getting Error when trying to run hisat2 script! Please help!

Question

[smithkthedale]

I have tried to create a hisat2 script loops and am encountering an error message and can't seem to figure where the problem is. Please help!

My script:

for i in $(<samples.txt)
do
        hisat2 -p 8 -x ./genome.index/GCA_002738505.1_Arabidopsis_thaliana_v1_genomic \
        -1 ${i}R1.cutadapt.fastq.bz2 -2 ${i}R2.cutadapt.fastq.bz2 -S ./sam.output/${i}sam --summary-file
        /RNAAtSeq/outputRNAAtSeq/sam.output/${i}summary.txt
done

Error: Extra parameter(s) specified:

"../outputRNAAtSeq/JRMM_RNAseq_MC_1_CCGCGGTT_Arabidopsis_I1187_L1.R2.cutadapt.fastq.bz2"

Error: Encountered internal HISAT2 exception (#1)
Command: /n/helmod/apps/centos7/Core/hisat2/2.1.0-fasrc01/hisat2-align-s --wrapper basic-0 -p 12 -x ./genome.index/GCA_002738505.1_Arabidopsis_thaliana_v1_genomic --rna-strandness RF -S ../outputRNAAtSeq/JRMM_RNAseq_MC_1_CCGCGGTT_Arabidospsis_I1187_L1.sam --summary-file ../outputRNAAtSeq/JRMM_RNAseq_MC_1_CCGCGGTT_Arabidopsis_I1187_L1.summary.txt -2 ../outputRNAAtSeq/JRMM_RNAseq_MC_1_CCGCGGTT_Arabidopsis_I1187_L1.R2.cutadapt.fastq.bz2 

(ERR): hisat2-align exited with value 1

[GenoMax]

${i}R1.cutadapt.fastq.bz2

hisat2 likely does not understand bz compression. Stay with standard bgzip/gzip or use process substitution to uncompress on fly.

[smithkthedale]

hisat2 should take bz compression...but if I were to change, how do I turn them into bgzip files? New to coding.

[ATpoint]

The error message and your command do not match. E.g. there is -1 missing in the error, also mismatch -p (8 vs 12) etc. So there is probably a copy/paste error on your side.

[smithkthedale]

Now I get: /var/slurmd/spool/slurmd/job16133235/slurm_script: line 17 when I fix it

[ATpoint]

There is no point showing slurm-related errors. Make a minimal testing dataset, de-loop the code and test it manually until it works. Then loop over tiny test datasets until it works. Once that is ok go to the cluster with the full data.

[Pierre Lindenbaum]

for i in $(<samples.txt)

you should use a workflow manager like snakemake or nextflow;