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ITBE-Lab / MA

The Modular Aligner and The Modular SV Caller
MIT License
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Index out of range exception for paired end reads #8

Closed dawnmy closed 3 years ago

dawnmy commented 3 years ago

I was trying to run MA on paired end short reads with:

$ maCMD -x dbs/ma.json -p Illumina_Paired -i datasets/short_read.qc_1.fq -m datasets/short_read.qc_2.fq -o outputs/metax.pe.sam

But I got the error below:

starting alignment.
Drop exception (different thread threw already): Index out of range
Drop exception (different thread threw already): Index out of range
Drop exception (different thread threw already): Index out of range
Throw exception
Error:
Index out of range

It was fine with single end file or comma separated list of files.

MarkusRainerSchmidt commented 3 years ago

Your command looks like it should work just fine.

Can you give me the two read-files you are using and tell me the commit you are working with? Without that, I won't be able to figure out what causes the error. My email is: schmidtm@hanyang.ac.kr

dawnmy commented 3 years ago

I used the version from bioconda:

ma   1.1.1  py37h8270d21_1  bioconda

I have send you the minimal example PE reads files per email.

MarkusRainerSchmidt commented 3 years ago

To summarize our e-mail correspondence:

I couldn't reproduce the error on my end, but version 1.1.2 (https://github.com/ITBE-Lab/MA/commit/96ebb636f3828b83a35fb52c76aeb7852c37198b) seems to resolve the problem.

Therefore, I'll close this issue for now.