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. — Reply to this email directly, view it on GitHub <#503 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACTBRQQ4SVDJGA4QJICEHVDUZIX2RANCNFSM5NBGSSEQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>