hicAggregateContacts: list index out of range

[Lucas446]

Hi,

I am using HiCexplorer hicAggregateContacts function to get the contacts between a set of genomic positions (.bed file).

head of my bed file:

chr3R 11371536 11373001
chr3R 16249423 16250737
chr3R 30911966 30912930
chr3R 16811677 16812290
chr3R 8181381 8182042
chr3R 7000639 7001267
chr3R 7037218 7037914
chr3R 16899483 16900033
chr3R 16829995 16830605
chr3R 4852336 4852868

first line of the validPair.bam:

NB551631:263:HTCJYAFX3:1:11101:17094:1026 81 chr3R 17458342 60 4S71M chr3L 8205337 0 TGATCGATCTCAACGAAGCATTCATATCGATATGCAGCCAGTATTAAATGCAATTTATGCAAATTTTTGNCATCA E/<EEAEAEEE/EEEEA/A/EEEAEE6EEEEE/EEEEEE/EE//EE//EEAE/EEEAEE/E///EE/EE#AAA/A NM:i:1 MD:Z:65C5 AS:i:69 XS:i:0

HiCexplorer command for hicAggregateContacts:

hicAggregateContacts -m ${FILE} --outFileName norm_smallest_esc_CyO_St10_St14cat_st10_25000bp_norm_ICE_autoCorr --BED ${BED} --mode ${MODE[1]} --range ${RANGE} --numberOfBins ${NUMBERofBINS} --transform ${TRAN[2]} --operationType ${OPTYPE[1]} --largeRegionsOperation ${LRO[0]} --outFilePrefixMatrix norm_smallest_esc_CyO_St10_St14cat_st10_25000bp_norm_ICE_autoCorr --outFileContactPairs ContactPairs --outFileObsExp FileObsExp --diagnosticHeatmapFile diagnosticHeatmapFile --chromosomes chr3R

The h5 resolution is 5000bp
RANGE="300000:1000000"
NUMBERofBINS=30

Here is the error I get:

Traceback (most recent call last):
File "/opt/miniconda3/envs/HiCexplorer_env/bin/hicAggregateContacts", line 7, in
main()
File "/opt/miniconda3/envs/HiCexplorer_env/lib/python3.9/site-packages/hicexplorer/hicAggregateContacts.py", line 915, in main
bed_intervals = read_bed_per_chrom(args.BED, chrom_list, args.considerStrandDirection)
File "/opt/miniconda3/envs/HiCexplorer_env/lib/python3.9/site-packages/hicexplorer/hicAggregateContacts.py", line 254, in read_bed_per_chrom
if fields[0] not in chrom_list:
IndexError: list index out of range

I don't understand what is wrong,

Thanks for your help,
Best,
Tanguy

[lldelisle]

Hi,
You may have an empty line in your file. Could you do a tail of your bed file?
Thanks

[Lucas446]

Hi Lucille, Thanks a lot for your reply, that was actually this issue :) Best, Tanguy Le ven. 4 nov. 2022 à 02:20, Lucille Delisle ***@***.***> a écrit :

…

Hi, You may have an empty line in your file. Could you do a tail of your bed file? Thanks — Reply to this email directly, view it on GitHub <#825 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALDDXRSUZOAJMUPGEDQF6X3WGSTMTANCNFSM6AAAAAARWQ6B3I> . You are receiving this because you authored the thread.Message ID: ***@***.***>