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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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bowtie2-align died with signal 7 (BUS) #644

Open mengying0714 opened 3 weeks ago

mengying0714 commented 3 weeks ago

hello, I ran the HIC-pro 3.1 on my server, and I got an error about bowtie2-align died with signal 7 (BUS)

I build bowtie2 index by myself, it returns an error about bowtie2 index. Then I download bowtie2 index from website(https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml), it return an error： bowtie2-align died with signal 7 (BUS)

cat 78M_L1_R2_bowtie2.log

HiC-Pro mapping

(ERR): bowtie2-align died with signal 7 (BUS)

cat 78M_L1_R1_bowtie2.log

HiC-Pro mapping

(ERR): bowtie2-align died with signal 7 (BUS)

cat mapping_step1.log /software/hicpro/3.1.0/envs/HiC-Pro_v3.1.0/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/78M_L1/78M_L1_R1_grch38_1kgmaj.bwt2glob.unmap.fastq --rg-id BMG --rg SM:78M_L1_R1 -p 2 -x /gpfs/fs2/scratch/public/mzh103/Hi-C/01.ref/hg38-bowtie2/grch38_1kgmaj -U rawdata/78M_L1/78M_L1_R1.fastq.gz 2>> logs/78M_L1/78M_L1_R1_bowtie2.log| /software/hicpro/3.1.0/envs/HiC-Pro_v3.1.0/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/78M_L1/78M_L1_R1_grch38_1kgmaj.bwt2glob.bam /software/hicpro/3.1.0/envs/HiC-Pro_v3.1.0/bin/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un bowtie_results/bwt2_global/78M_L1/78M_L1_R2_grch38_1kgmaj.bwt2glob.unmap.fastq --rg-id BMG --rg SM:78M_L1_R2 -p 2 -x /gpfs/fs2/scratch/public/mzh103/Hi-C/01.ref/hg38-bowtie2/grch38_1kgmaj -U rawdata/78M_L1/78M_L1_R2.fastq.gz 2>> logs/78M_L1/78M_L1_R2_bowtie2.log| /software/hicpro/3.1.0/envs/HiC-Pro_v3.1.0/bin/samtools view -F 4 -bS - > bowtie_results/bwt2_global/78M_L1/78M_L1_R2_grch38_1kgmaj.bwt2glob.bam

The commnd: HiC-Pro -i /public/mzh103/Hi-C/02.fasta/78M -o /public/mzh103/Hi-C/mapping -c /public/mzh103/Hi-C/config-hicpro.txt

I also unload the config-hicpro.txt file. config-hicpro.txt
Do you have any mind on the issue?

nservant commented 1 week ago

I guess this is more a bowtie2 issue. Can you try to run it without HiC-Pro ?

mengying0714 commented 6 days ago

Thank you for your reply, it has worked. Have a nice day!

发件人: Nicolas Servant @.> 发送时间: 2024年9月23日 4:58 收件人: nservant/HiC-Pro @.> 抄送: Zhang, Mengying @.>; Author @.> 主题: [EXT] Re: [nservant/HiC-Pro] bowtie2-align died with signal 7 (BUS) (Issue #644)

I guess this is more a bowtie2 issue. Can you try to run it without HiC-Pro ?

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