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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
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Error reading _ftab[] array #317

Open adamfreedman opened 2 years ago

adamfreedman commented 2 years ago

Genome index built (with same version of hisat2 as used for alignment) using basic build cmd (as I've done many times before)...and without any errors. For what it's worth, the genome is highly fragmented and hisat2 constructs a long index. Upon attempting alignment, getting very sparse error message.

I run the following cmd: hisat2 -p 16 -x /n/holyscratch01/informatics/adamf/trifrog/genomes/hisat2/bullfrog/v3/RC-genome-V3-20170621.submission -q --phred33 -1 ${1}_1.fastq -2 ${1}2.fastq -S bullfrog${1}_hisat2.sam

where $1 is an SRA accession id embedded in the fastq files. An example error:

Error reading _ftab[] array: 3904, 8194 Error: Encountered internal HISAT2 exception (#1) Command: /n/home_rc/afreedman/.conda/envs/hisat2/bin/hisat2-align-l --wrapper basic-0 -p 16 -x /n/holyscratch01/informatics/adamf/trifrog/genomes/hisat2/bullfrog/v3/RC-genome-V3-20170621.submission -q --phred33 -S bullfrog_SRR2086385_hisat2.sam --read-lengths 100 -1 SRR2086385_1.fastq -2 SRR2086385_2.fastq (ERR): hisat2-align exited with value 1

In the absence of more detailed error info, no idea what is going on here.

adamfreedman commented 2 years ago

I should also note, that a subsequent submission on the same fastq files yields a slightly different error: Error reading _offs[] array: 0, 190

parkchanhee commented 2 years ago

@adamfreedman It seems that the index file is not built correctly. Could you build an index again and upload the terminal output of the command?

adamfreedman commented 2 years ago

attached is the log for the original index build build.log

adamfreedman commented 2 years ago

I did not mean to close this ... sorry.

adamfreedman commented 2 years ago

just checking if there is any progress on figuring out what is going on with this particular error?

parkchanhee commented 2 years ago

@adamfreedman Sorry for the late response. Typically, this error is caused by the corrupted index file. There are many reasons for a file broken. The index file may be overwritten by other HISAT2 build process.

I have successfully built the index using same reference. (I downloaded the reference from https://www.bcgsc.ca/downloads/supplementary/bullfrog/. It seems to be a same file you used. If not, could you send me a link where I can download it. I'll try to build it)

And, could you send the each index file size and their hash value( the result of md5sum command)?