bowtie2-align died with signal 7 (BUS)

[mengying0714]

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]

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

[mengying0714]

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 ? ― Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/nservant/HiC-Pro/issues/644*issuecomment-2367606622__;Iw!!MkQhnT5yHH0MPvOc00c!TXUhNQGNSXuu4IyW_qsuAzUJcjE-MtGZYMF_w0mze_8aZ3Pf6nr0Ec42_HQFfwIrvX88ryWzwiwkoFwDuW6vNtPJRNrvApvdaS7Djsw$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BK3EDNXN2AKPQHKBBG2IIEDZX7J3NAVCNFSM6AAAAABNUSVY4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRXGYYDMNRSGI__;!!MkQhnT5yHH0MPvOc00c!TXUhNQGNSXuu4IyW_qsuAzUJcjE-MtGZYMF_w0mze_8aZ3Pf6nr0Ec42_HQFfwIrvX88ryWzwiwkoFwDuW6vNtPJRNrvApvdtVWdGYA$>. You are receiving this because you authored the thread.Message ID: ***@***.***>