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dan-landau / IronThrone-GoT

processes GoT amplicon data and generates a table of metrics
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fastq.gz error #2

Open petervangalen opened 4 years ago

petervangalen commented 4 years ago

Hey, Great work!

I noticed that when I use .fastq.gz files I get the error "Illegal modulus zero at /home/unix/vangalen/IronThrone/IronThrone-GoT line 2048."

IronThrone-GoT --run linear --config TET2.4104.config --fastqR1 BPDCN712-GoT-Rxn4_R1.fastq.gz --fastqR2 BPDCN712-GoT-Rxn4_R2.fastq.gz --umilen 12 --whitelist ~/IronThrone-GoT-master/barcodes10X/3M-february-2018.txt --outdir TET2.4104 --log GoT_TET2.4104.log --sample TET2.4104

When I first gunzip the fastqs I don't get that error.

dan-landau commented 3 years ago

Hello!

This is definitely a known issue, we are working on resolving it in future updates. For now, if possible, using unzipped fastqs is best.

Lipinski-B commented 3 years ago

Hi @petervangalen, hi @landau-lab,

After few test, this error (that I also had) has maybe no matter with the zipped or unzipped fastqs. I think It's also about a bad calculation using the number of thread and the number of barecodes available to use in the whitelist file. I try with a number of 8000 and 5000 cells barecodes inside the whitelist file and it works, but 10 000 doesn't work, with 5700 or both whitelists files given in the "barcodes10X" directory neither, I still had this error!! So I don't understand... Probably a problem about a modulus calculation in relation with the manipulation of the thread's number variable and the number of barecode inside the whitelist, as maybe the line 2048 tends to say us...

Hope the developpers will find a solution soon. Best, Boris

jkmorrison commented 7 months ago

Hi @dan-landau ,

Was this issue ever resolved? I'm trying to use GoT but am stuck on this same error.

Best, Josh

RebeccaMurray commented 7 months ago

Hi @jkmorrison! Are you getting this error even with gunzipped fastq files? Please feel free to reach out to rmurray@nygenome.org and we can help resolve the issue. Thanks, Rebecca