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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Read Pairs Alignment on Restriction Fragments 100% dumped #458

Closed yinshiyi closed 3 years ago

yinshiyi commented 3 years ago

Hi,

My bowtie2 was fine with 60% unique aligned but then in the hindiii fragment bed file part, 100% of the reads pairs were dumped

Any ideas? Thank you. Also got an error saying

Run quality checks for all samples ... Logs: logs/sample2/make_Rplots.log make: *** [/usr/local/bin/HiC-Pro_3.0.0/bin/../scripts//Makefile:181: hic_qc] Error 1

yinshiyi commented 3 years ago

/usr/bin/python /usr/local/bin//HiC-Pro_3.0.0/scripts/mapped_2hic_fragments.py -v -a -f /home/shiyi/pig_DpnII.bed -r bowtie_results/bwt2/sample1/_Sscrofa11.1.bwt2pairs.bam -o hic_results/data/sample1 [E::idx_find_and_load] Could not retrieve index file for 'bowtie_results/bwt2/sample1/_Sscrofa11.1.bwt2pairs.bam'

overlapMapped2HiCFragments.py

mappedReadsFile= bowtie_results/bwt2/sample1/_Sscrofa11.1.bwt2pairs.bam

fragmentFile= /home/shiyi/pig_DpnII.bed

minInsertSize= None

maxInsertSize= None

minFragSize= None

maxFragSize= None

allOuput= True

SAM ouput= False

verbose=True

Loading Restriction File Intervals /home/shiyi/pig_DpnII.bed ...

load_restriction_fragment function took 63384.249ms

Opening SAM/BAM file bowtie_results/bwt2/sample1/_Sscrofa11.1.bwt2pairs.bam ...

Classifying Interactions ...

Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1509:35537 at NC_010457.5 : 112159388 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1509:35537 at NC_010457.5 : 112159050 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1803:37840 at NC_010443.5 : 28984637 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1803:37840 at NC_010443.5 : 28984696 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1966:43220 at NC_010450.4 : 89508133 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1966:43220 at NC_010450.4 : 89507958 Warning - no restriction fragments for GWNJ-0850:721:GW2002102893rd:2:1101:1976:20700 at NC_010443.5 : 219511418