make: *** [bowtie_global] Error 1

[NZhang487]

Hello!

First of all, thank you for developing this amazing tool!

I'm new to hic analysis and was trying to run HiC-Pro 3.0.0 on the test dataset. Here is my command: /data/huangfu/ZhangN/bin/HiC-Pro-3.0.0/bin/HiC-Pro -c config_test_latest.txt -i test_data -o hicpro_latest_test

I run it on a cluster and got the following error message:

Run HiC-Pro 3.0.0

Sat Jul 24 21:05:23 EDT 2021 Bowtie2 alignment step1 ... Logs: /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/logs/dixon_2M_2/mapping_step1.log Exit: Error in reads alignment - Exit make: *** [bowtie_global] Error 1

Here are my log files:

cat mapping_step1.log /home/zhangn2/bin/bowtie2-2.4.4/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R1_hg19.bwt2glob.unmap.fastq --rg-id BMG --rg SM:SRR400264_01_R1 -p 1 -x /lila/data/leslie/genome_index/hg19.bowtie2/hg19 -U rawdata/dixon_2M_2/SRR400264_01_R1.fastq.gz 2>> /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/logs/dixon_2M_2/SRR400264_01_R1_bowtie2.log| /opt/common/CentOS_7/samtools/samtools-1.8/bin/samtools view -F 4 -bS - > /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R1_hg19.bwt2glob.bam /home/zhangn2/bin/bowtie2-2.4.4/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R2_hg19.bwt2glob.unmap.fastq --rg-id BMG --rg SM:SRR400264_01_R2 -p 1 -x /lila/data/leslie/genome_index/hg19.bowtie2/hg19 -U rawdata/dixon_2M_2/SRR400264_01_R2.fastq.gz 2>> /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/logs/dixon_2M_2/SRR400264_01_R2_bowtie2.log| /opt/common/CentOS_7/samtools/samtools-1.8/bin/samtools view -F 4 -bS - > /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R2_hg19.bwt2glob.bam

cat SRR400264_01_R2_bowtie2.log

HiC-Pro mapping

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

I tried to directly run bowtie2 on the test fastq files and it worked fine. So it seems not a problem with bowtie2... Do you have any idea what is going wrong here?

Thanks a lot for your help! Nan

[nservant]

Hi, It seems that this is more a bowtie2 issue than a HiC-pro one. If you goodle the error "(ERR): bowtie2-align died with signal 7 (BUS)", you may find some help. Maybe corrupted index files ? https://github.com/FelixKrueger/Bismark/issues/339 N

[NZhang487]

Hi, Thank you for your prompt reply! I tried to regenerate bowtie2 index, but still got the same error. I even tried to reinstall HiC-Pro, but it did not help either. The strange thing is that when I directly run bowtie2 on the files, I can generate the output files without any error:

[zhangn2@lilac-ln02 ES]$ /home/zhangn2/bin/bowtie2-2.4.4/bowtie2 --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder --un /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R2_hg19.bwt2glob.unmap.fastq --rg-id BMG --rg SM:SRR400264_01_R2 -p 1 -x /data/huangfu/ZhangN/genome/hg19/hg19 -U test_data/dixon_2M_2/SRR400264_01_R2.fastq.gz 2>> /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/logs/dixon_2M_2/SRR400264_01_R2_bowtie2.log| /opt/common/CentOS_7/samtools/samtools-1.8/bin/samtools view -F 4 -bS - > /data/huangfu/ZhangN/HiCAR/ES/hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/SRR400264_01_R2_hg19.bwt2glob.bam

[zhangn2@lilac-ln02 ES]$ ll hicpro_latest_test/bowtie_results/bwt2_global/dixon_2M_2/ total 15441 -rw-r--r-- 1 zhangn2 huangfu 62 Jul 25 16:44 SRR400264_01_R1_hg19.bwt2glob.bam -rw-r--r-- 1 zhangn2 huangfu 0 Jul 25 16:44 SRR400264_01_R1_hg19.bwt2glob.unmap.fastq -rw-r--r-- 1 zhangn2 huangfu 8699402 Jul 25 16:46 SRR400264_01_R2_hg19.bwt2glob.bam -rw-r--r-- 1 zhangn2 huangfu 7108574 Jul 25 16:46 SRR400264_01_R2_hg19.bwt2glob.unmap.fastq

I'm confused ...

[nservant]

And if you try to run bowtie2 on the cluster ?

[NZhang487]

Yes, directly running bowtie2 on the cluster can generate the output bam file.

[mengying0714]

Hello, I got the same error, Do you know the wrong reason? Thank you.