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churchill-lab / kallisto-align

Export kallisto pseudo-alignments in a sparse binary matrix format
http://churchill-lab.github.io/kallisto-align/
GNU General Public License v2.0
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error performing kallisto-align #2

Open mfrancesconi81 opened 6 years ago

mfrancesconi81 commented 6 years ago

Hi KB,

I tried getting sparse matrix files using kallisto-align. I run kallisto index using the kallisto distributed with kallisto-align with no problems then I run kallisto-align like this

kallisto-align -f ${FASTQ_DIR}'A6M-2_21583_TAGCTT.fastq.gz' -i ${EMASE_DIR}'emase.pooled.targets.kallisto.index' -b ${EMASE_DIR}'A6M-2_21583_TAGCTT.bin'

and I got the following error

terminate called after throwing an instance of 'std::regex_error' what(): regex_error Aborted (core dumped)

Any clue?

Thanks,

Mirko

kbchoi-jax commented 6 years ago

It seems like there's some parsing error. Could you focus on using g2gtools, alntools, and then emase-zero for now so we can check if your initial steps are fine? I will test kallisto-align myself when I have a chance.