How to build hisat2 index on scaffold level genome assembly

0

Entering edit mode

4.3 years ago

tulika98 • 0

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 • 861 views

ADD COMMENT • link updated 4.3 years ago by ATpoint 82k • written 4.3 years ago by tulika98 • 0

0

Entering edit mode

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

ADD REPLY • link 4.3 years ago by ATpoint 82k

0

Entering edit mode

There are no files in this folder.

ADD REPLY • link 4.3 years ago by tulika98 • 0

0

Entering edit mode

...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.

ADD REPLY • link 4.3 years ago by ATpoint 82k

0

Entering edit mode

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.

ADD REPLY • link 4.3 years ago by tulika98 • 0

0

Entering edit mode

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.

ADD REPLY • link 4.3 years ago by ATpoint 82k

0

Entering edit mode

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

ADD REPLY • link 4.3 years ago by tulika98 • 0

0

Entering edit mode

Any suggusteions will be helpful? @ATpoint?

ADD REPLY • link 4.3 years ago by tulika98 • 0

0

Entering edit mode

Job ID Name User Time Use S Queue

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

ADD REPLY • link 4.3 years ago by tulika98 • 0

Login before adding your answer.