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hicMergeDomains bug: `list index out of range`
Hi
me again sorry. I am again unlucky with my first try of hicMergeDomains (3.7.2)
Traceback (most recent call last):
File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/bin/hicMergeDomains", line 7, in <module>
main()
File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 428, in main
create_tree(relationList, mergedListWithId, args.outputTreePlotPrefix, args.outputTreePlotFormat)
File "/g/funcgen/gbcs/public/software/conda/envs/hicexplorer-3.7.2/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 280, in create_tree
while int(sList[posSList][1][0][3:]) < int(rList[posRList][1][3:]):
IndexError: list index out of range
thx
能否请您提供您使用的命令行
This software you have developed is fantastic! But I have a problem when I use the hicMergeDomains to merge TAD files in multiple resolutions, how should I solve it?
hicexplorer=3.7.2 python=3.8.8
hicMergeDomains --domainFiles ../fat_5000_Normalize_domains.bed ../fat_10000_Normalize_domains.bed ../fat_25000_Normalize_domains.bed ../fat_50000_Normalize_domains.bed
Saved relation tree of NC_052532.1
Saved relation tree of NC_052533.1
Saved relation tree of NC_052534.1
Traceback (most recent call last):
File "/home/SLY68/anaconda3/bin/hicMergeDomains", line 7, in <module>
main()
File "/home/SLY68/anaconda3/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 428, in main
create_tree(relationList, mergedListWithId, args.outputTreePlotPrefix, args.outputTreePlotFormat)
File "/home/SLY68/anaconda3/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 280, in create_tree
while int(sList[posSList][1][0][3:]) < int(rList[posRList][1][3:]):
IndexError: list index out of range
Also, the error reported when I add a CTGF file using the -p:
hicMergeDomains --domainFiles ../fat_5000_Normalize_domains.bed ../fat_10000_Normalize_domains.bed ../fat_25000_Normalize_domains.bed ../fat_50000_Normalize_domains.bed -p ./CTCF.Broad.Peaks.bed
Traceback (most recent call last):
File "/home/SLY68/anaconda3/bin/hicMergeDomains", line 7, in <module>
main()
File "/home/SLY68/anaconda3/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 415, in main
mergedList = create_list_with_protein(args.domainFiles[0], args.minimumNumberOfPeaks, proteinList)
File "/home/SLY68/anaconda3/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 399, in create_list_with_protein
bList = compare_boundaries_protein(bList, cList)
File "/home/SLY68/anaconda3/lib/python3.8/site-packages/hicexplorer/hicMergeDomains.py", line 374, in compare_boundaries_protein
if posTad < len(bList) and chromPosition < len(cList) and bList[posTad][0] != cList[chromPosition][0][0]:
IndexError: list index out of range
Contents of the file CTCF.Broad.Peaks.bed
$ head CTCF.Broad.Peaks.bed:
NC_052533.1 12768909 12768943 CTGF_1 - - 37.4128 1.48e-15 3.07e-06
NC_052554.1 3560877 3560911 CTGF_2 - + 36.5688 6.5e-15 5.06e-06
NC_052538.1 36329267 36329301 CTGF_3 - - 36.367 9.07e-15 5.06e-06
NC_052536.1 26271359 26271393 CTGF_4 - + 36.2569 1.08e-14 5.06e-06
NC_052549.1 11566318 11566352 CTGF_5 - + 36.0367 1.54e-14 5.06e-06
NC_052540.1 23679796 23679830 CTGF_6 - - 35.844 2.08e-14 5.06e-06
NC_052539.1 29527143 29527177 CTGF_7 - - 35.844 2.08e-14 5.06e-06
NC_052545.1 47679 47713 CTGF_8 - + 35.844 2.08e-14 5.06e-06
NC_052543.1 20072122 20072156 CTGF_9 - - 35.8073 2.2e-14 5.06e-06
NC_052549.1 8808877 8808910 CTGF_10 - - 34.4797 2.37e-14 1.21e-05
Had the same issue but found a solution that maybe can help you as well.
if posTad < len(bList) and chromPosition < len(cList) and bList[posTad][0] != cList[chromPosition][0][0]: IndexError: list index out of range
I realized I had the coordinates of some scaffold-chromosomes in one file but not in others.
Be sure that all chromosomes present in --proteinFile are also found in --domainFiles and vice versa. If hicMergeDomains fails to find a correspondence, it will output that error.
If all chromosomes are matched, it should work. Another possibility, if you cannot avoid having discrepancies between the two file-types, would be to process each chromosome separately.
Hope this can help you!
Hi, I am having the same problem but I am not using --proteinFile. I am just using --domainFiles produced by the hicMergeTADS function. _domain.bed files that use 1MB, 100KB, 50KB work fine but I get the error below when using 40KB and 20KB _domain.bed files.
$hicMergeDomains --domainFiles IMR90_Wt.1000000_balanced_hicfindtads_domains.bed IMR90_Wt.100000_balanced_hicfindtads_domains.bed IMR90_Wt.50000_balanced_hicfindtads_domains.bed IMR90_Wt.40000_balanced_hicfindtads_domains.bed
Saved relation tree of chr1
Saved relation tree of chr2
Traceback (most recent call last):
File "/home/users/ashbym/miniconda3/envs/hic_explorer/bin/hicMergeDomains", line 7, in
It would be great if someone could suggest a fix. Thanks!
What is the difference between these files? Try to check if TADs called at different resolutions have some differences in terms of chromosomes.
I have no idea why this would happen, but just to be sure try to double check it using:
cat ${FILE} | cut -f 1 | sort | uniq
on all input files, and see if something pops out
Thanks for the advice. I did check the chromosome names and all were normal 'chrN' and matching in each 'domainFiles'. I added some extra debugging output and it looks like the 'sList' that holds TAD info for each chromosome was empty. This only occurred when I included 'domainFiles' with larger bins (1mb to 50kb) along with smaller bins (40kb, 20kb) AND the larger bin domainFiles were listed first in the 'hicMergeDomains' command. When I change the order of the 'domainFiles' so that the smaller bin files are at the beginning then 'hicMergeDomains' command works fine. I am not really sure why. So..
Outputs "IndexError: list index out of range" error
hicMergeDomains --domainFiles IMR90_Wt.1000000_balanced_hicfindtads_domains.bed IMR90_Wt.100000_balanced_hicfindtads_domains.bed IMR90_Wt.50000_balanced_hicfindtads_domains.bed IMR90_Wt.40000_balanced_hicfindtads_domains.bed IMR90_Wt.20000_balanced_hicfindtads_domains.bed
No error
hicMergeDomains --domainFiles IMR90_Wt.20000_balanced_hicfindtads_domains.bed IMR90_Wt.40000_balanced_hicfindtads_domains.bed IMR90_Wt.50000_balanced_hicfindtads_domains.bed IMR90_Wt.100000_balanced_hicfindtads_domains.bed IMR90_Wt.1000000_balanced_hicfindtads_domains.bed
@ashbymorrison Hello, I have encountered the same problem. Have you found a solution？ There are such problems either in order of resolution data from small to large or in order of resolution data from large to small bin
In my case, the error seemed to be resolved when listing the bins in order of small bins to large bins in the —hicMergeTADS function. When I listed large bins first then small bins I would get the error.
On Mar 15, 2024, at 7:28 PM, HaiTao Zhu @.***> wrote:
@ashbymorrison https://github.com/ashbymorrison Hello, I have encountered the same problem. Have you found a solution？ There are such problems either in order of resolution data from small to large or in order of resolution data from large to small bin
— Reply to this email directly, view it on GitHub https://github.com/deeptools/HiCExplorer/issues/790#issuecomment-2001204416, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKCSKOTBWP2K6NDDH3VYPQDYYOU5JAVCNFSM5SI7RNVKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMBQGEZDANBUGE3A. You are receiving this because you were mentioned.
In my case, the error seemed to be resolved when listing the bins in order of small bins to large bins in the —hicMergeTADS function. When I listed large bins first then small bins I would get the error. … On Mar 15, 2024, at 7:28 PM, HaiTao Zhu @.***> wrote: @ashbymorrison https://github.com/ashbymorrison Hello, I have encountered the same problem. Have you found a solution？ There are such problems either in order of resolution data from small to large or in order of resolution data from large to small bin — Reply to this email directly, view it on GitHub <#790 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKCSKOTBWP2K6NDDH3VYPQDYYOU5JAVCNFSM5SI7RNVKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMBQGEZDANBUGE3A. You are receiving this because you were mentioned.
Thx, But that didn't solve my situation,and i check the chromosome names too