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How to build hisat2 index on scaffold level genome assembly

Hi everyone,

I am trying to build hisat2 index for a yeast strain called RM11-1A. The reference genome is available in scaffolds at:

https://downloads.yeastgenome.org/sequence/strains/RM11-1a/RM11-1A_SGD_2015_JRIP00000000/

I have downloaded the reference genome and ran the code below. However, I don't get any index files in the folder. The output and error files are both empty. I can't figure out what is the problem. Any help is greatly appreciated.

hisat2-build -p 8 -f /scratch/ts00010/genome/RM11-1A_SGD_2015_JRIP00000000.fsa /scratch/ts00010/genome/hisat2_RM11_1A_index/RM11-1A_hisat2_index
rna-seq assembly alignment sequencing genome
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updated by ATpoint ATpoint • written by tulika98 • tulika98

Output of ls /scratch/ts00010/genome/hisat2_RM11_1A_index/?

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written by ATpoint ATpoint

There are no files in this folder.

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written by tulika98 • tulika98

...and did the job run, did you get the status update from that tool, or did is crash? Without more info it is difficult to help.

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written by ATpoint ATpoint

I can submit the job. I get a job id and it shows hat the job status as 'C' i.e. complete, with a 0:0:0 runtime.

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written by tulika98 • tulika98

So nothing is happening. Does the output folder exist? Test your script with a dummy fasta file, like a single entry and see if that works. Please show a head of the fasta file.

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written by ATpoint ATpoint

The code works for another strain of yeast (S288c) that I am working with.

The header of S288C:

ref|NC_001133| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=I] CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT

The header of RM11:

gi|696445000|gb|JRIP01000001.1| Saccharomyces cerevisiae strain RM11-1A scaffold-0, whole genome sequence TTAAGCCTTCAAAGAAGAAGCTCTTCTCTTTCTGATTTCGGCCTTTTCAGCCTTTCTTTCAGACAATCTCTTAGCCAACA ATTGAGCGTATTCGGCAGCAGCTTCTCTTTGAGCTTGAGCGTTTCTGACCTTCAAAGCTCTTTGGTGTCTCTTTCTTTGC

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written by tulika98 • tulika98

Any suggusteions will be helpful? @ATpoint?

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written by tulika98 • tulika98

Job ID Name User Time Use S Queue

155803.trcis002.hpc.wvu.edu ...t2_build_rm11 ts00010 00:00:00 C comm_small_day

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written by tulika98 • tulika98

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