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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Bowtie2 alignment step1 ... Logs: logs/Control1/mapping_step1.log #624

Closed Woogle90 closed 6 months ago

Woogle90 commented 6 months ago

I am running hic-pro in the foreground. The only message I got is this: Run HiC-Pro 3.1.0 Sun Mar 10 10:41:48 CST 2024 Bowtie2 alignment step1 ... Logs: logs/Control1/mapping_step1.log

And then the program seems to be "sleeping" (ps STAT is S), with no ERROR, no WARNING, no EXIT (no OUTPUT of course). In fact, it has been sleeping for the whole night.....

Here is the mapping_step1.log: /lustre/home/acct-yuewujess/zchiang/.conda/envs/test-env/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/Control1/control1_R2_GRCh38.p14.genome.bwt2glob.unmap.fastq --rg-id BMG --rg SM:control1_R2 -p 2 -x /lustre/home/acct-yuewujess/zchiang/2307nature/GRCh38.p14.genome -U rawdata/Control1/control1_R2.fastq.gz 2>> logs/Control1/control1_R2_bowtie2.log| /lustre/home/acct-yuewujess/zchiang/.conda/envs/test-env/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/Control1/control1_R2_GRCh38.p14.genome.bwt2glob.bam /lustre/home/acct-yuewujess/zchiang/.conda/envs/test-env/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/Control1/control1_R1_GRCh38.p14.genome.bwt2glob.unmap.fastq --rg-id BMG --rg SM:control1_R1 -p 2 -x /lustre/home/acct-yuewujess/zchiang/2307nature/GRCh38.p14.genome -U rawdata/Control1/control1_R1.fastq.gz 2>> logs/Control1/control1_R1_bowtie2.log| /lustre/home/acct-yuewujess/zchiang/.conda/envs/test-env/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/Control1/control1_R1_GRCh38.p14.genome.bwt2glob.bam

Due to the authority limitation, I have to run hic-pro in the conda test environment.

Any possible reasons of this situation?

Woogle90 commented 6 months ago

I checked the size of bwt2_global folder in the OUTPUT and it is increasing. I take it that the program is still running but it may takes a real long time. I close this issue for now.