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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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/Makefile:144: bowtie_pairing] Error 1 #445

Closed gaoyuanccc closed 3 years ago

gaoyuanccc commented 3 years ago

Hello, I have a problem with Pairing of R1 and R2 tags ... My error is as follows：

Pairing of R1 and R2 tags ... Logs: logs/m1/mergeSAM.log make: *** [/home/gaoyuan/HiC/HiC-Pro_3.0.0/bin/../scripts//Makefile:144: bowtie_pairing] Error 1

I checked mergesam.log content is as follows：

[E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/m1/m1_TKD181102273_R1.clean_sc19.bwt2merged.bam' [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/m1/m1_TKD181102273_R2.clean_sc19.bwt2merged.bam'

mergeBAM.py

forward= bowtie_results/bwt2/m1/m1_TKD181102273_R1.clean_sc19.bwt2merged.bam

reverse= bowtie_results/bwt2/m1/m1_TKD181102273_R2.clean_sc19.bwt2merged.bam

output= bowtie_results/bwt2/m1/m1_TKD181102273.clean_sc19.bwt2pairs.bam

min mapq= 10

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.

I don't know what's wrong with my files? How can I solve this problem? Thanks for any answers!

gaoyuanccc commented 3 years ago

how to check my .bam files

Peggy1998 commented 10 months ago

I meet the same question, how can I solve it ?