mergeSAM.log error

[hcsun1]

Dear HiC-Pro Authors,

Thank you for your software. However, I encountered an error while running my own data:

Pairing of R1 and R2 tags ... Logs: logs/Fuji/mergeSAM.log Makefile:144: bowtie_pairing] Error 1

Upon further investigation, I found the following error in the mergeSAM.log file.

I have tried many solutions, including installing the HiC-Pro Singularity image, but I still haven't been able to resolve this issue.

Could you kindly assist me with this problem? I greatly appreciate your help.

Best regards, Haochen Sun

[nservant]

Could you check the read names in R1/R2 files. They should be identical, and it seems that recently some sequencers add /1, /2 at the end of the read names .... which make HiC-Pro crashing

[qqyanyang]

Could you check the read names in R1/R2 files. They should be identical, and it seems that recently some sequencers add /1, /2 at the end of the read names .... which make HiC-Pro crashing

Excuse me，I have a same error when I running HiC-pro process. My error like this: Run HiC-Pro 3.1.0

Bowtie2 alignment step1 ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_step1.log

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Bowtie2 alignment step2 ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_step2.log

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Combine R1/R2 alignment files ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_combine.log

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Mapping statistics for R1 and R2 tags ... Logs: logs/iPSC_P13_Hi-C_R1r1/mapping_stats.log

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Pairing of R1 and R2 tags ... Logs: logs/iPSC_P13_Hi-C_R1r1/mergeSAM.log make: *** [path../../HiC-Pro_3.1.0/bin/../scripts//Makefile:144: bowtie_pairing] Error 1

And this is my mergeSAMlog: python_path/../bin/python /../HiC-Pro_3.1.0/scripts/mergeSAM.py -q 0 -t -v -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam -r bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_hg38.bwt2pairs.bam [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam' [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam'

mergeBAM.py

forward= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam

reverse= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam

output= bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_hg38.bwt2pairs.bam

min mapq= 0

report_single= False

report_multi= False

verbose= True

Merging forward and reverse tags ...

Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted.

And my mapping_conbine.log is : ../bin/samtools merge -@ 144 -n -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam bowtie_results/bwt2_global/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2glob.bam bowtie_results/bwt2_local/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2glob.unmap_bwt2loc.bam ../bin/samtools merge -@ 144 -n -f bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam bowtie_results/bwt2_global/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2glob.bam bowtie_results/bwt2_local/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2glob.unmap_bwt2loc.bam ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_1_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_2_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam ../bin/HiC-Pro_3.1.0/scripts/hic.inc.sh: Line 86: 2519760 Killed ../bin/samtools sort -@ 144 -m 1000M -n -T tmp/iPSC_P13_Hi-C_R1r1_1_hg38 -o bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_1_hg38.bwt2merged.bam [bam_sort_core] merging from 288 files and 144 in-memory blocks... mv bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.sorted.bam bowtie_results/bwt2/iPSC_P13_Hi-C_R1r1/iPSC_P13_Hi-C_R1r1_2_hg38.bwt2merged.bam

With your answer for hcsun1, I while try your solvement, but how can I check the read names in my files? Like that: iPSC_P13_Hi-C_R1r1_1.fq.gz iPSC_P13_Hi-C_R1r1_2.fq.gz If you need the config-hicpro.txt ,I while support it.Thanks a lot