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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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how to index bam files after sorting by reads name ? #612

Open wu123tj opened 5 months ago

wu123tj commented 5 months ago

hi,nservant: i met an error when running mergeSAM.py as follows: /share/nas1/xiazb/02.soft/conda/conda3/envs/hicpro/bin/python /share/nas1/xiazb/02.soft/HiC-Pro/HiC-Pro_3.1.0/scripts/mergeSAM.py -q 10 -t -v -f bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.bam -r bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.bam -o bowtie_results/bwt2/rename/BM089_BM089.bwt2pairs.bam [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.bam' [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.bam'

mergeBAM.py

forward= bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.bam

reverse= bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.bam

output= bowtie_results/bwt2/rename/BM089_BM089.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.

the BM089_R1_BM089.bwt2merged.bam was sorted successly :

/share/nas1/xiazb/02.soft/cactus-bin-v2.5.0/bin/samtools sort -@ 10 -m 1000M -n -T tmp/BM089_R1_BM089 -o bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.sorted.bam bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.bam /share/nas1/xiazb/02.soft/cactus-bin-v2.5.0/bin/samtools sort -@ 10 -m 1000M -n -T tmp/BM089_R2_BM089 -o bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.sorted.bam bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.bam [bam_sort_core] merging from 160 files and 10 in-memory blocks... [bam_sort_core] merging from 160 files and 10 in-memory blocks... mv bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.sorted.bam bowtie_results/bwt2/rename/BM089_R1_BM089.bwt2merged.bam mv bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.sorted.bam bowtie_results/bwt2/rename/BM089_R2_BM089.bwt2merged.bam

when checking the command samtools sort -n , it shows than sorting by read name is not compatible with samtools index command

how to index bam files after sorting by reads name , sence mergeSAM.py requires an index file ?

nservant commented 5 months ago

Hi, mergeSAM.py requires the reads to be in the same order. I do not think the index is mandatory here N