search

liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
277 stars 48 forks source link

TRUST4 crash no reason #156

Open Chuang1118 opened 2 years ago

Chuang1118 commented 2 years ago

Hello trust4,

Version TRUST4 use Output all the required fields for AIRR format https://github.com/liulab-dfci/TRUST4/pull/138

CMD

run-trust4 -f {params.REF1} -t 24 --ref {params.REF2} \
    -u {input.fastq1} \
    --barcode {input.fastq2} \
    --barcodeRange 0 7 + \
    --barcodeWhitelist {params.BARCODE} \
    --UMI {input.fastq2} --umiRange 8 15 + \
    -o {wildcards.sample} --od `dirname {output}` --repseq

BUG: In time point [Wed Sep 28 22:22:50 2022] is blank.

[Wed Sep 28 22:16:19 2022] Read in and count kmers for 11900000 reads. [Wed Sep 28 22:16:23 2022] Read in and count kmers for 12000000 reads. [Wed Sep 28 22:16:26 2022] Read in and count kmers for 12100000 reads. [Wed Sep 28 22:22:50 2022]

cmd observed in server & I have enough RAM & Mem image image

reRUN same CMD, this time is work fine. [Thu Sep 29 12:07:01 2022] Read in and count kmers for 11900000 reads. [Thu Sep 29 12:07:04 2022] Read in and count kmers for 12000000 reads. [Thu Sep 29 12:07:07 2022] Read in and count kmers for 12100000 reads. [Thu Sep 29 12:13:47 2022] Found 12156257 reads. [Thu Sep 29 12:14:12 2022] Finish sorting the reads.

I counter this issue both in ref mouse & human.

Please advise me,

Chuang

mourisl commented 2 years ago

I think the read in and count kmer is not the sophisticated part, and should not crash normally. I feel this is more like a system error. Did you run TRUST4 on a cluster and when rerun the cmd is it on the same node?

Chuang1118 commented 2 years ago

I use TRUST4 by building singularity container and launch job by Snakemake, because I've also gene expression part. Now, I am in stage define parameters hardware in multiple cores server. I have tested 2 servers, I counter this problem 1 time for human, 1 time for mouse. This error is not reproducible. Run and reRun are in same server. I plan to run TRUST4 in HPC Slurm, since my lab production many BCR data.

mourisl commented 2 years ago

I'm not familiar with the containers, and there could be some issues with virtualization. Please let me know if it still crashes running on slurm without singularity.