Hello,
I am getting an error when running HISAT2 using hg19 full specifically as the genome. When HISAT2 is run using hg19 canonical or hg38, the job completed without any issues. I re-ran HISAT2 on a previously completed job using hg19 full, and it throws an error. The error seems to be stemming from the hg19 index on CVMFS. I am posting the error and the command used below:
Error reading _ebwt[] array: 14118, 15360
Error: Encountered internal HISAT2 exception (#1)
Command: /home/galaxyp_user/galaxyp/galaxy/database/dependencies/_conda/envs/mulled-v1-ad7c0e574419219598c842c5e534a388c10d33e19c5718205a00928715733608/bin/hisat2-align-s --wrapper basic-0 -p 1 -x /cvmfs/data.galaxyproject.org/managed/hisat2_index/hg19/hg19 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --dta --read-lengths 151 -1 /tmp/3452387.inpipe1 -2 /tmp/3452387.inpipe2
(ERR): hisat2-align exited with value 1
samtools sort: failed to read header from "-"
[main_samview] fail to read the header from "-".
The command is as follows:
set -o pipefail; ln -f -s '/home/galaxyp_user/galaxyp/galaxy/database/objects/d/2/b/dataset_d2b3484d-ef9f-4e56-9735-2d45a1493ed3.dat' input_f.fastq.gz && ln -f -s '/home/galaxyp_user/galaxyp/galaxy/database/objects/d/a/5/dataset_da5930b7-36d4-467e-afe4-76062554ab50.dat' input_r.fastq.gz && hisat2 -p ${GALAXY_SLOTS:-1} -x '/cvmfs/data.galaxyproject.org/managed/hisat2_index/hg19/hg19' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --dta | samtools sort --no-PG -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/home/galaxyp_user/galaxyp/galaxy/database/objects/e/a/c/dataset_eacad32c-e139-4a60-a286-a364d28d6d70.dat'
My research keeps pointing to a corrupt hg19 index file. When tested using command line interface and point Galaxy and HISAT2 to use local hg19 indexed files (downloaded from Index of /managed/hisat2_index/hg19/), it does not throw an error which suggests that the hg19 index on CVMFS seems to be corrupt.
Since we are running a local Galaxy instance and use CVMFS, is there a way to unmount and remount CVMFS to correct this issue?
Any other suggestions that you may have to solve this?
Thanks
icon) of a prior job? Do both ways fail, or just one of those? Which?
You could disconnect and reconnect, and the server should be restarted after added in local indexes (ancillary to CVMFS) but I’m assuming you have done that already.
