Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

hg38 panel of normals not working #141

Open
denbogdan opened this issue Jan 28, 2025 · 0 comments
Open

hg38 panel of normals not working #141

denbogdan opened this issue Jan 28, 2025 · 0 comments

Comments

@denbogdan
Copy link

When I try to run ichorCNA against my hg38 aligned data with the provided hg38 references, including the PoN, I run into this error over and over again. Could anyone help me find out what the issue is?

gc="gc_hg38_500kb.wig"
map="map_hg38_500kb.wig"
centromere="GRCh38.GCA_000001405.2_centromere_acen.txt"
normal="HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds"	
	
Rscript $ichor --id sample \
  --WIG sample.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 \
  --gcWig $gc \
  --mapWig $map \
  --centromere $centromere \
  --normalPanel $normal \
  --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" \
  --estimateNormal True --estimatePloidy True --estimateScPrevalence True \
  --scStates "c(1,3)" --txnE 0.9999 --txnStrength 10000 --outDir .

This is the error I get:

Loading tumour file:sample
Slurping: sample.wig
Parsing: fixedStep chrom=1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=10 start=1 step=500000 span=500000
Parsing: fixedStep chrom=11 start=1 step=500000 span=500000
Parsing: fixedStep chrom=12 start=1 step=500000 span=500000
Parsing: fixedStep chrom=13 start=1 step=500000 span=500000
Parsing: fixedStep chrom=14 start=1 step=500000 span=500000
Parsing: fixedStep chrom=15 start=1 step=500000 span=500000
Parsing: fixedStep chrom=16 start=1 step=500000 span=500000
Parsing: fixedStep chrom=17 start=1 step=500000 span=500000
Parsing: fixedStep chrom=18 start=1 step=500000 span=500000
Parsing: fixedStep chrom=19 start=1 step=500000 span=500000
Parsing: fixedStep chrom=2 start=1 step=500000 span=500000
Parsing: fixedStep chrom=20 start=1 step=500000 span=500000
Parsing: fixedStep chrom=21 start=1 step=500000 span=500000
Parsing: fixedStep chrom=22 start=1 step=500000 span=500000
Parsing: fixedStep chrom=3 start=1 step=500000 span=500000
Parsing: fixedStep chrom=4 start=1 step=500000 span=500000
Parsing: fixedStep chrom=5 start=1 step=500000 span=500000
Parsing: fixedStep chrom=6 start=1 step=500000 span=500000
Parsing: fixedStep chrom=7 start=1 step=500000 span=500000
Parsing: fixedStep chrom=8 start=1 step=500000 span=500000
Parsing: fixedStep chrom=9 start=1 step=500000 span=500000
Parsing: fixedStep chrom=MT start=1 step=16569 span=16569
Parsing: fixedStep chrom=X start=1 step=500000 span=500000
Parsing: fixedStep chrom=Y start=1 step=500000 span=500000
Parsing: fixedStep chrom=KI270728.1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=KI270727.1 start=1 step=448248 span=448248
Parsing: fixedStep chrom=KI270442.1 start=1 step=392061 span=392061
Parsing: fixedStep chrom=KI270729.1 start=1 step=280839 span=280839
Parsing: fixedStep chrom=GL000225.1 start=1 step=211173 span=211173
Parsing: fixedStep chrom=KI270743.1 start=1 step=210658 span=210658
Parsing: fixedStep chrom=GL000008.2 start=1 step=209709 span=209709
Parsing: fixedStep chrom=GL000009.2 start=1 step=201709 span=201709
Parsing: fixedStep chrom=KI270747.1 start=1 step=198735 span=198735
Parsing: fixedStep chrom=KI270722.1 start=1 step=194050 span=194050
Parsing: fixedStep chrom=GL000194.1 start=1 step=191469 span=191469
Parsing: fixedStep chrom=KI270742.1 start=1 step=186739 span=186739
Parsing: fixedStep chrom=GL000205.2 start=1 step=185591 span=185591
Parsing: fixedStep chrom=GL000195.1 start=1 step=182896 span=182896
Parsing: fixedStep chrom=KI270736.1 start=1 step=181920 span=181920
Parsing: fixedStep chrom=KI270733.1 start=1 step=179772 span=179772
Parsing: fixedStep chrom=GL000224.1 start=1 step=179693 span=179693
Parsing: fixedStep chrom=GL000219.1 start=1 step=179198 span=179198
Parsing: fixedStep chrom=KI270719.1 start=1 step=176845 span=176845
Parsing: fixedStep chrom=GL000216.2 start=1 step=176608 span=176608
Parsing: fixedStep chrom=KI270712.1 start=1 step=176043 span=176043
Parsing: fixedStep chrom=KI270706.1 start=1 step=175055 span=175055
Parsing: fixedStep chrom=KI270725.1 start=1 step=172810 span=172810
Parsing: fixedStep chrom=KI270744.1 start=1 step=168472 span=168472
Parsing: fixedStep chrom=KI270734.1 start=1 step=165050 span=165050
Parsing: fixedStep chrom=GL000213.1 start=1 step=164239 span=164239
Parsing: fixedStep chrom=GL000220.1 start=1 step=161802 span=161802
Parsing: fixedStep chrom=KI270715.1 start=1 step=161471 span=161471
Parsing: fixedStep chrom=GL000218.1 start=1 step=161147 span=161147
Parsing: fixedStep chrom=KI270749.1 start=1 step=158759 span=158759
Parsing: fixedStep chrom=KI270741.1 start=1 step=157432 span=157432
Parsing: fixedStep chrom=GL000221.1 start=1 step=155397 span=155397
Parsing: fixedStep chrom=KI270716.1 start=1 step=153799 span=153799
Parsing: fixedStep chrom=KI270731.1 start=1 step=150754 span=150754
Parsing: fixedStep chrom=KI270751.1 start=1 step=150742 span=150742
Parsing: fixedStep chrom=KI270750.1 start=1 step=148850 span=148850
Parsing: fixedStep chrom=KI270519.1 start=1 step=138126 span=138126
Parsing: fixedStep chrom=GL000214.1 start=1 step=137718 span=137718
Parsing: fixedStep chrom=KI270708.1 start=1 step=127682 span=127682
Parsing: fixedStep chrom=KI270730.1 start=1 step=112551 span=112551
Parsing: fixedStep chrom=KI270438.1 start=1 step=112505 span=112505
Parsing: fixedStep chrom=KI270737.1 start=1 step=103838 span=103838
Parsing: fixedStep chrom=KI270721.1 start=1 step=100316 span=100316
Parsing: fixedStep chrom=KI270738.1 start=1 step=99375 span=99375
Parsing: fixedStep chrom=KI270748.1 start=1 step=93321 span=93321
Parsing: fixedStep chrom=KI270435.1 start=1 step=92983 span=92983
Parsing: fixedStep chrom=GL000208.1 start=1 step=92689 span=92689
Parsing: fixedStep chrom=KI270538.1 start=1 step=91309 span=91309
Parsing: fixedStep chrom=KI270756.1 start=1 step=79590 span=79590
Parsing: fixedStep chrom=KI270739.1 start=1 step=73985 span=73985
Parsing: fixedStep chrom=KI270757.1 start=1 step=71251 span=71251
Parsing: fixedStep chrom=KI270709.1 start=1 step=66860 span=66860
Parsing: fixedStep chrom=KI270746.1 start=1 step=66486 span=66486
Parsing: fixedStep chrom=KI270753.1 start=1 step=62944 span=62944
Parsing: fixedStep chrom=KI270589.1 start=1 step=44474 span=44474
Parsing: fixedStep chrom=KI270726.1 start=1 step=43739 span=43739
Parsing: fixedStep chrom=KI270735.1 start=1 step=42811 span=42811
Parsing: fixedStep chrom=KI270711.1 start=1 step=42210 span=42210
Parsing: fixedStep chrom=KI270745.1 start=1 step=41891 span=41891
Parsing: fixedStep chrom=KI270714.1 start=1 step=41717 span=41717
Parsing: fixedStep chrom=KI270732.1 start=1 step=41543 span=41543
Parsing: fixedStep chrom=KI270713.1 start=1 step=40745 span=40745
Parsing: fixedStep chrom=KI270754.1 start=1 step=40191 span=40191
Parsing: fixedStep chrom=KI270710.1 start=1 step=40176 span=40176
Parsing: fixedStep chrom=KI270717.1 start=1 step=40062 span=40062
Parsing: fixedStep chrom=KI270724.1 start=1 step=39555 span=39555
Parsing: fixedStep chrom=KI270720.1 start=1 step=39050 span=39050
Parsing: fixedStep chrom=KI270723.1 start=1 step=38115 span=38115
Parsing: fixedStep chrom=KI270718.1 start=1 step=38054 span=38054
Parsing: fixedStep chrom=KI270317.1 start=1 step=37690 span=37690
Parsing: fixedStep chrom=KI270740.1 start=1 step=37240 span=37240
Parsing: fixedStep chrom=KI270755.1 start=1 step=36723 span=36723
Parsing: fixedStep chrom=KI270707.1 start=1 step=32032 span=32032
Parsing: fixedStep chrom=KI270579.1 start=1 step=31033 span=31033
Parsing: fixedStep chrom=KI270752.1 start=1 step=27745 span=27745
Parsing: fixedStep chrom=KI270512.1 start=1 step=22689 span=22689
Parsing: fixedStep chrom=KI270322.1 start=1 step=21476 span=21476
Parsing: fixedStep chrom=GL000226.1 start=1 step=15008 span=15008
Parsing: fixedStep chrom=KI270311.1 start=1 step=12399 span=12399
Parsing: fixedStep chrom=KI270366.1 start=1 step=8320 span=8320
Parsing: fixedStep chrom=KI270511.1 start=1 step=8127 span=8127
Parsing: fixedStep chrom=KI270448.1 start=1 step=7992 span=7992
Parsing: fixedStep chrom=KI270521.1 start=1 step=7642 span=7642
Parsing: fixedStep chrom=KI270581.1 start=1 step=7046 span=7046
Parsing: fixedStep chrom=KI270582.1 start=1 step=6504 span=6504
Parsing: fixedStep chrom=KI270515.1 start=1 step=6361 span=6361
Parsing: fixedStep chrom=KI270588.1 start=1 step=6158 span=6158
Parsing: fixedStep chrom=KI270591.1 start=1 step=5796 span=5796
Parsing: fixedStep chrom=KI270522.1 start=1 step=5674 span=5674
Parsing: fixedStep chrom=KI270507.1 start=1 step=5353 span=5353
Parsing: fixedStep chrom=KI270590.1 start=1 step=4685 span=4685
Parsing: fixedStep chrom=KI270584.1 start=1 step=4513 span=4513
Parsing: fixedStep chrom=KI270320.1 start=1 step=4416 span=4416
Parsing: fixedStep chrom=KI270382.1 start=1 step=4215 span=4215
Parsing: fixedStep chrom=KI270468.1 start=1 step=4055 span=4055
Parsing: fixedStep chrom=KI270467.1 start=1 step=3920 span=3920
Parsing: fixedStep chrom=KI270362.1 start=1 step=3530 span=3530
Parsing: fixedStep chrom=KI270517.1 start=1 step=3253 span=3253
Parsing: fixedStep chrom=KI270593.1 start=1 step=3041 span=3041
Parsing: fixedStep chrom=KI270528.1 start=1 step=2983 span=2983
Parsing: fixedStep chrom=KI270587.1 start=1 step=2969 span=2969
Parsing: fixedStep chrom=KI270364.1 start=1 step=2855 span=2855
Parsing: fixedStep chrom=KI270371.1 start=1 step=2805 span=2805
Parsing: fixedStep chrom=KI270333.1 start=1 step=2699 span=2699
Parsing: fixedStep chrom=KI270374.1 start=1 step=2656 span=2656
Parsing: fixedStep chrom=KI270411.1 start=1 step=2646 span=2646
Parsing: fixedStep chrom=KI270414.1 start=1 step=2489 span=2489
Parsing: fixedStep chrom=KI270510.1 start=1 step=2415 span=2415
Parsing: fixedStep chrom=KI270390.1 start=1 step=2387 span=2387
Parsing: fixedStep chrom=KI270375.1 start=1 step=2378 span=2378
Parsing: fixedStep chrom=KI270420.1 start=1 step=2321 span=2321
Parsing: fixedStep chrom=KI270509.1 start=1 step=2318 span=2318
Parsing: fixedStep chrom=KI270315.1 start=1 step=2276 span=2276
Parsing: fixedStep chrom=KI270302.1 start=1 step=2274 span=2274
Parsing: fixedStep chrom=KI270518.1 start=1 step=2186 span=2186
Parsing: fixedStep chrom=KI270530.1 start=1 step=2168 span=2168
Parsing: fixedStep chrom=KI270304.1 start=1 step=2165 span=2165
Parsing: fixedStep chrom=KI270418.1 start=1 step=2145 span=2145
Parsing: fixedStep chrom=KI270424.1 start=1 step=2140 span=2140
Parsing: fixedStep chrom=KI270417.1 start=1 step=2043 span=2043
Parsing: fixedStep chrom=KI270508.1 start=1 step=1951 span=1951
Parsing: fixedStep chrom=KI270303.1 start=1 step=1942 span=1942
Parsing: fixedStep chrom=KI270381.1 start=1 step=1930 span=1930
Parsing: fixedStep chrom=KI270529.1 start=1 step=1899 span=1899
Parsing: fixedStep chrom=KI270425.1 start=1 step=1884 span=1884
Parsing: fixedStep chrom=KI270396.1 start=1 step=1880 span=1880
Parsing: fixedStep chrom=KI270363.1 start=1 step=1803 span=1803
Parsing: fixedStep chrom=KI270386.1 start=1 step=1788 span=1788
Parsing: fixedStep chrom=KI270465.1 start=1 step=1774 span=1774
Parsing: fixedStep chrom=KI270383.1 start=1 step=1750 span=1750
Parsing: fixedStep chrom=KI270384.1 start=1 step=1658 span=1658
Parsing: fixedStep chrom=KI270330.1 start=1 step=1652 span=1652
Parsing: fixedStep chrom=KI270372.1 start=1 step=1650 span=1650
Parsing: fixedStep chrom=KI270548.1 start=1 step=1599 span=1599
Parsing: fixedStep chrom=KI270580.1 start=1 step=1553 span=1553
Parsing: fixedStep chrom=KI270387.1 start=1 step=1537 span=1537
Parsing: fixedStep chrom=KI270391.1 start=1 step=1484 span=1484
Parsing: fixedStep chrom=KI270305.1 start=1 step=1472 span=1472
Parsing: fixedStep chrom=KI270373.1 start=1 step=1451 span=1451
Parsing: fixedStep chrom=KI270422.1 start=1 step=1445 span=1445
Parsing: fixedStep chrom=KI270316.1 start=1 step=1444 span=1444
Parsing: fixedStep chrom=KI270340.1 start=1 step=1428 span=1428
Parsing: fixedStep chrom=KI270338.1 start=1 step=1428 span=1428
Parsing: fixedStep chrom=KI270583.1 start=1 step=1400 span=1400
Parsing: fixedStep chrom=KI270334.1 start=1 step=1368 span=1368
Parsing: fixedStep chrom=KI270429.1 start=1 step=1361 span=1361
Parsing: fixedStep chrom=KI270393.1 start=1 step=1308 span=1308
Parsing: fixedStep chrom=KI270516.1 start=1 step=1300 span=1300
Parsing: fixedStep chrom=KI270389.1 start=1 step=1298 span=1298
Parsing: fixedStep chrom=KI270466.1 start=1 step=1233 span=1233
Parsing: fixedStep chrom=KI270388.1 start=1 step=1216 span=1216
Parsing: fixedStep chrom=KI270544.1 start=1 step=1202 span=1202
Parsing: fixedStep chrom=KI270310.1 start=1 step=1201 span=1201
Parsing: fixedStep chrom=KI270412.1 start=1 step=1179 span=1179
Parsing: fixedStep chrom=KI270395.1 start=1 step=1143 span=1143
Parsing: fixedStep chrom=KI270376.1 start=1 step=1136 span=1136
Parsing: fixedStep chrom=KI270337.1 start=1 step=1121 span=1121
Parsing: fixedStep chrom=KI270335.1 start=1 step=1048 span=1048
Parsing: fixedStep chrom=KI270378.1 start=1 step=1048 span=1048
Parsing: fixedStep chrom=KI270379.1 start=1 step=1045 span=1045
Parsing: fixedStep chrom=KI270329.1 start=1 step=1040 span=1040
Parsing: fixedStep chrom=KI270419.1 start=1 step=1029 span=1029
Parsing: fixedStep chrom=KI270336.1 start=1 step=1026 span=1026
Parsing: fixedStep chrom=KI270312.1 start=1 step=998 span=998
Parsing: fixedStep chrom=KI270539.1 start=1 step=993 span=993
Parsing: fixedStep chrom=KI270385.1 start=1 step=990 span=990
Parsing: fixedStep chrom=KI270423.1 start=1 step=981 span=981
Parsing: fixedStep chrom=KI270392.1 start=1 step=971 span=971
Parsing: fixedStep chrom=KI270394.1 start=1 step=970 span=970
Sorting by decreasing chromosome size
Reading GC and mappability files
Slurping: gc_hg38_500kb.wig
Parsing: fixedStep chrom=chr1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr2 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr3 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr4 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr5 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr6 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr7 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr8 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr9 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr10 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr11 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr12 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr13 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr14 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr15 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr16 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr17 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr18 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr19 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr20 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr21 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr22 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chrX start=1 step=500000 span=500000
Parsing: fixedStep chrom=chrY start=1 step=500000 span=500000
Sorting by decreasing chromosome size
Slurping: map_hg38_500kb.wig
Parsing: fixedStep chrom=chr1 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr2 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr3 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr4 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr5 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr6 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr7 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr8 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr9 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr10 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr11 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr12 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr13 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr14 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr15 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr16 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr17 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr18 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr19 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr20 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr21 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chr22 start=1 step=500000 span=500000
Parsing: fixedStep chrom=chrX start=1 step=500000 span=500000
Parsing: fixedStep chrom=chrY start=1 step=500000 span=500000
Sorting by decreasing chromosome size
Correcting Tumour
Removed 193 bins near centromeres.
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Filtering low uniqueness regions with mappability score < 0.9
Removed 1 bins near centromeres.
Determining gender...Gender male
Outputting to: .//sample.correctedDepth.txt
Warning message:
In regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
runEM: Initialization
runEM iter1: Expectation
runEM iter1: Maximization
Error in rho[, 1] : subscript out of bounds
Calls: HMMsegment -> runEM -> estimateParamsMap
Execution halted
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@denbogdan