combine error

[seasky002002]

the program hangup when running combine bams, here are the logs, Thu Jan 27 20:11:41 CST 2022 Combine R1/R2 alignment files ... Logs: logs/rep1/mapping_combine.log make: *** [/usr/local/bin/HiC-Pro_2.11.4/bin/../scripts//Makefile:115: bowtie_com bine] Error 129 Hangup

And the mapping_combine.log only has two lines: more result/logs/rep1/mapping_combine.log /usr/local/anaconda/bin/samtools merge -@ 2 -n -f bowtie_results/bwt2/rep1/SRR401 5027_pass_2_hg19.bwt2merged.bam bowtie_results/bwt2_global/rep1/SRR4015027_pass_2 _hg19.bwt2glob.bam bowtie_results/bwt2_local/rep1/SRR4015027_pass_2_hg19.bwt2glob .unmap_bwt2loc.bam /usr/local/anaconda/bin/samtools merge -@ 2 -n -f bowtie_results/bwt2/rep1/SRR401 5027_pass_1_hg19.bwt2merged.bam bowtie_results/bwt2_global/rep1/SRR4015027_pass_1 _hg19.bwt2glob.bam bowtie_results/bwt2_local/rep1/SRR4015027_pass_1_hg19.bwt2glob .unmap_bwt2loc.bam

Would you please help me to debug? Thank you!

[nservant]

Do you have the bwt2merged.bam files ? otherwise, my feeling is that you had a memory issue with the samtools merge command.

[seasky002002]

I have 2 replicates, but only have the bwt2merged.bam files for replicate #1. You can find the bwt2merged.bam files here, https://vanderbilt.box.com/s/ma4tjc6m8z81tr4pgvuvg53kmbjbavso

Thank you!

On Thursday, February 3, 2022, Nicolas Servant @.***> wrote:

Do you have the bwt2merged.bam files ? otherwise, my feeling is that you had a memory issue with the samtools merge command.

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