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AlgoLab / galig

A graph aligner
GNU General Public License v3.0
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Asgal (from run in your provided docker): doesn't find Transcript file, looks for gtf instead. #10

Closed amitfenn closed 4 years ago

amitfenn commented 4 years ago

Hi Luca,

It's me again, I ran ASGAL on the docker you gave me and I seem to be coming up with an issue that took me a while to fix, because of a misguiding error message:

Starting ASGAL run for /MOUNT/input/fastq/subsample_15_100K_1.fastq and /MOUNT/input/fastq/subsample_15_100K_2.fastq ...
[ Oct 28, 2020 -  2:28:46PM ] args Namespace(allevents=False, annoPath='/MOUNT/input/splicing_variants.gtf', debug=False, e='3', l='15', multiMode=True, outputPath='/MOUNT/output/asgal-output/subsample_15_100K_1-output', refPath='/MOUNT/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa', sample1Path='/MOUNT/input/fastq/subsample_15_100K_1.fastq', sample2Path='/MOUNT/input/fastq/subsample_15_100K_2.fastq', split_only=False, threads='6', transPath='/MOUNT/input/custom_transcripts.fasta', verbose=False, w='3')

Transcripts file /MOUNT/input/splicing_variants.gtf not found. Halting...

I have no name!@061a56a9b51a:/$ ls /MOUNT/input/splicing_variants.gtf
/MOUNT/input/splicing_variants.gtf

I had the transcript file missing... but it told me that the gtf was missing. I just solved this after I posted the issue here.. :P I'll close this issue.. but please note the misguiding error message.

ldenti commented 4 years ago

fae7119b2349320681a7a2b2f95578b322b50c7d fixes the error message. Thanks for pointing this out