Error with overlapping gaps when running PureCN #339
Comments
|
Hi @akaviaLab . never seen this one before. You are using a slightly older version. Don't think it's fixed, but you can easily update with: BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18") Does it work with the GATK segmentation (Needs the gatk binary in path)? It's probably better for lower coverage WES anyways. Markus |
|
I'll try it with the newer version and with GATK segmentation. I assume that means using GATK4 as the segmentation function, correct? Thank you! |
|
Yes, it looks like the Inf values causing issues are generated somehow by the PSCBS segmentation. I would need debug data to dig deeper. Let me know if you can share minimal data to make it reproducible and I'll send you a link to upload. But if GATK works, you should be fine. Correct, just GATK as segmentation function. That particular sample is ~70X. It's fine for WES, but most use PureCN with targeted panels at much higher coverage and PSCBS is tuned mostly on those samples. |
|
You can also try turning off off-target reads. They don't help much with WES. There is a parameter to specify the minimum fraction of intervals being off-target. If that fixes things, there might be something wrong with the interval file (although would be weird if your current setup works on some samples as you indicate). |
|
I've seen an issue where you recommend setting this parameter as 1 (I think
#279), but is there an intermediate
value you'd recommend?
Also, I have a mixture of coverage - some genes should reach around X400 or
so. If that's the case, is using GATK still a good idea?
Thank you very much!
…On Tue, Dec 19, 2023 at 4:10 PM Markus Riester ***@***.***> wrote:
You can also try turning off off-target reads. They don't help much with
WES. There is a parameter to specify the minimum fraction of intervals
being off-target. If that fixes things, there might be something wrong with
the interval file (although would be weird if that works on some samples as
you indicate).
—
Reply to this email directly, view it on GitHub
<#339 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ACQYYZQ4WPMRW4OHBHQIWLTYKG4ATAVCNFSM6AAAAABA26DTMOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRTGA3DAOBQGU>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
Anything higher than what you have works. 228926 on-target, 16245 off-target, so even 0.1 would do. yes, GATK should still be fine. |
Describe the issue
Running PureCN on a sample fails with Detected overlapping gaps on chromosome , : INTERNAL ERROR: Detected overlapping gaps on chromosome 10 in argument gaps . Calls: runAbsoluteCN ... gapsToSegments.data.frame -> throw -> throw.default
This is a Paired End sample, where I stitched the reads together using BBMerge before aligning, variant calling and PureCN.
To Reproduce
Copy and paste your complete command line arguments from PureCN.R. If possible and potentially relevant, also copy the output of NormalDB.R and Coverage.R.
Coverage.R
exit $rcINFO [2023-12-18 15:47:33] Loading PureCN 1.22.2...
INFO [2023-12-18 15:47:33] Processing /home/dnanexus/work/out/ewes-heme-001_markdup.recalibrated_coverage.txt.gz...
[W::hts_idx_load2] The index file is older than the data file: /home/dnanexus/inputs/input17659710669220063763/ewes-heme-001_markdup.recalibrated.bam.bai
Warning messages:Dec 18 2023, 4:02 PM
1: stat_contour(): Zero contours were generated
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
4: stat_contour(): Zero contours were generated
5: In min(x) : no non-missing arguments to min; returning Inf
6: In max(x) : no non-missing arguments to max; returning -Inf
7: Removed 1 row(s) containing missing values (geom_path).
PureCN.R
Rscript /usr/local/lib/R/site-library/PureCN/extdata/PureCN.R --force --postoptimize --seed 123 --outvcf --funsegmentation PSCBS --genome hg38 --sampleid pureCN_ewes-heme-001 --tumor out/ewes-heme-001_markdup.recalibrated_coverage_loess.txt.gz --vcf /home/dnanexus/inputs/input17659710669220063763/ewes-heme-001_markdup.recalibrated_mutect2_unfiltered-final-annotation.vcf.gz --mappingbiasfile /home/dnanexus/inputs/input17659710669220063763/mapping_bias_eWES_heme_merge_hg38_PON_hg38.rds --normaldb /home/dnanexus/inputs/input17659710669220063763/normalDB_eWES_neogenomics_hg38_merged_hg38.rds --intervals /home/dnanexus/inputs/input17659710669220063763/eWES_neogenomics_hg38_merged_probes_intervals.withGenes.txt --out pureCN_ewes-heme-001
Expected behavior
A clear and concise description of what you expected to happen.
Log file
INFO [2023-12-18 16:02:12] Loading PureCN 1.22.2...
INFO [2023-12-18 16:02:21] Mean coverages: chrX: 35.90, chrY: 36.46, chr1-22: 61.30.
INFO [2023-12-18 16:02:21] Sample sex: M
INFO [2023-12-18 16:02:22] ------------------------------------------------------------
INFO [2023-12-18 16:02:22] PureCN 1.22.2
INFO [2023-12-18 16:02:22] ------------------------------------------------------------
INFO [2023-12-18 16:02:22] Arguments: -tumor.coverage.file /home/dnanexus/work/out/ewes-heme-001_markdup.recalibrated_coverage_loess.txt.gz -log.ratio -seg.file -vcf.file /home/dnanexus/inputs/input17659710669220063763/ewes-heme-001_markdup.recalibrated_mutect2_unfiltered-final-annotation.vcf.gz -genome hg38 -sex ? -args.setPriorVcf 6 -args.setMappingBiasVcf /home/dnanexus/inputs/input17659710669220063763/mapping_bias_eWES_heme_merge_hg38_PON_hg38.rds -args.filterIntervals 100 -args.segmentation 0.005,NULL, -sampleid pureCN_ewes-heme-001 -min.ploidy 1.4 -max.ploidy 6 -max.non.clonal 0.2 -max.homozygous.loss 0.05,1e+07 -log.ratio.calibration 0.1 -model.homozygous FALSE -error 0.001 -interval.file /home/dnanexus/inputs/input17659710669220063763/eWES_neogenomics_hg38_merged_probes_intervals.withGenes.txt -max.segments 300 -plot.cnv TRUE -vcf.field.prefix PureCN. -DB.info.flag DB -POPAF.info.field POP_AF -model beta -post.optimize TRUE -BPPARAM -log.file pureCN_ewes-heme-001.log -normal.coverage.file -normalDB -args.filterVcf -fun.segmentation -test.num.copy -test.purity -speedup.heuristics
INFO [2023-12-18 16:02:22] Loading coverage files...
INFO [2023-12-18 16:02:25] Mean target coverages: 72X (tumor) 91X (normal).
INFO [2023-12-18 16:02:26] Mean coverages: chrX: 35.90, chrY: 36.46, chr1-22: 61.30.
INFO [2023-12-18 16:02:27] Mean coverages: chrX: 32.16, chrY: 36.46, chr1-22: 61.27.
INFO [2023-12-18 16:02:42] Removing 733 intervals with missing log.ratio.
INFO [2023-12-18 16:02:42] Removing 3 low/high GC targets.
INFO [2023-12-18 16:02:43] Removing 4576 intervals excluded in normalDB.
INFO [2023-12-18 16:02:43] normalDB provided. Setting minimum coverage for segmentation to 0.0015X.
INFO [2023-12-18 16:02:43] Removing 9351 low coverage (< 0.0015X) intervals.
INFO [2023-12-18 16:02:43] Removing 11549 low count (< 100 total reads) intervals.
INFO [2023-12-18 16:02:43] Using 245171 intervals (228926 on-target, 16245 off-target).
INFO [2023-12-18 16:02:43] Ratio of mean on-target vs. off-target read counts: 0.64
INFO [2023-12-18 16:02:43] Mean off-target bin size: 112269
INFO [2023-12-18 16:02:44] AT/GC dropout: 1.01 (tumor), 1.06 (normal), 0.98 (coverage log-ratio).
INFO [2023-12-18 16:02:44] Loading VCF...
INFO [2023-12-18 16:02:52] Found 117065 variants in VCF file.
INFO [2023-12-18 16:02:53] Removing 6471 triallelic sites.
WARN [2023-12-18 16:02:53] VCF contains both DB and POPAF INFO fields. Will ignore POPAF.
INFO [2023-12-18 16:02:53] 49384 (44.7%) variants annotated as likely germline (DB INFO flag).
INFO [2023-12-18 16:02:55] ewes-heme-001 is tumor in VCF file.
INFO [2023-12-18 16:02:57] 589 homozygous and 143 heterozygous variants on chrX.
INFO [2023-12-18 16:02:57] Sex from VCF: M (Fisher's p-value: < 0.0001, odds-ratio: 6.99).
INFO [2023-12-18 16:02:57] Detected MuTect2 VCF.
INFO [2023-12-18 16:02:58] Removing 24823 Mutect2 calls due to blacklisted failure reasons.
INFO [2023-12-18 16:03:02] Initial testing for significant sample cross-contamination: unlikely
INFO [2023-12-18 16:03:03] Removing 47344 variants with AF < 0.030 or AF >= 0.970 or less than 3 supporting reads or depth < 15.
WARN [2023-12-18 16:03:03] Variant ids contain NAs at filter step BQ.
INFO [2023-12-18 16:03:03] Removing 0 low quality variants with BQ < 25.
INFO [2023-12-18 16:03:03] Total size of targeted genomic region: 41.36Mb (61.24Mb with 50bp padding).
INFO [2023-12-18 16:03:04] 11.9% of targets contain variants.
INFO [2023-12-18 16:03:04] Removing 8042 variants outside intervals.
INFO [2023-12-18 16:03:04] Setting somatic prior probabilities for dbSNP hits to 0.000500 or to 0.500000 otherwise.
INFO [2023-12-18 16:03:04] Loading mapping bias file mapping_bias_eWES_heme_merge_hg38_PON_hg38.rds...
INFO [2023-12-18 16:03:05] Found 459221 variants in mapping bias file.
INFO [2023-12-18 16:03:09] Imputing mapping bias for 3042 variants...
INFO [2023-12-18 16:04:15] Excluding 7952 novel or poor quality variants from segmentation.Dec 18 2023, 4:04 PM
INFO [2023-12-18 16:04:15] Sample sex: M
INFO [2023-12-18 16:04:15] Segmenting data...
INFO [2023-12-18 16:04:15] Interval weights found, will use weighted PSCBS.
INFO [2023-12-18 16:04:16] Setting undo.SD parameter to 0.750000.
INFO [2023-12-18 16:04:16] On-target much cleaner than off-target, finding on-target breakpoints first...
INFO [2023-12-18 16:04:16] Using 166683 high quality (out of 230168) on-target intervals for initial breakpoint calculation.
CPU: 7% (16 cores) * Memory: 4544/31066MB * Storage: 19/376GB * Net: 0↓/0↑MBps
INFO [2023-12-18 16:05:39] Setting prune.hclust.h parameter to 0.200000.
chromosome start end
1 1 -Inf 1776227.0
2 1 1776228.0 1858181.0
3 1 1858182.0 2184880.5
4 1 2184881.5 2203536.0
5 1 2203537.0 2543400.0
6 1 2543401.0 2587809.5
7 1 2587810.5 2587808.5
8 1 2587809.5 3045882.0
9 1 3045883.0 3045881.0
10 1 3045882.0 3448321.5
11 1 3448322.5 3664836.0
12 1 3664837.0 3742697.5
13 1 3742698.5 7771758.5
14 1 7771759.5 7886818.0
15 1 7886819.0 7886817.0
16 1 7886818.0 7950714.5
17 1 7950715.5 7950713.5
18 1 7950714.5 7994801.0
19 1 7994802.0 7994800.0
20 1 7994801.0 8166772.0
21 1 8166773.0 9666191.5
22 1 9666192.5 9728659.0
23 1 9728660.0 11103552.0
24 1 11103553.0 11179803.0
25 1 11179804.0 11179802.0
26 1 11179803.0 11197002.5
27 1 11197003.5 11674144.5
28 1 11674145.5 11684252.0
29 1 11684253.0 11790184.5
30 1 11790185.5 11804595.0
31 1 11804596.0 15433130.5
32 1 15433131.5 15454603.5
33 1 15454604.5 16125075.5
34 1 16125076.5 16151953.5
35 1 16151954.5 17018750.0
36 1 17018751.0 17061294.0
37 1 17061295.0 17621162.0
38 1 17621163.0 18557214.5
39 1 18557215.5 18557213.5
40 1 18557214.5 18792258.0
41 1 18792259.0 22774835.5
42 1 22774836.5 22933353.5
43 1 22933354.5 23544773.5
44 1 23544774.5 23719832.5
45 1 23719833.5 32261234.5
46 1 32261235.5 32333879.0
47 1 32333880.0 35146397.0
48 1 35146398.0 35230914.5
49 1 35230915.5 36178278.0
50 1 36178279.0 36305252.5
51 1 36305253.5 36305251.5
52 1 36305252.5 36334684.0
53 1 36334685.0 36334683.0
54 1 36334684.0 36377439.5
55 1 36377440.5 36377438.5
56 1 36377439.5 36465069.0
57 1 36465070.0 36465068.0
58 1 36465069.0 36642132.5
59 1 36642133.5 39890349.0
60 1 39890350.0 39928279.0
61 1 39928280.0 43330189.5
62 1 43330190.5 43352769.0
63 1 43352770.0 44817112.5
64 1 44817113.5 44846846.0
65 1 44846847.0 45328361.5
66 1 45328362.5 45340585.0
67 1 45340586.0 46039625.5
68 1 46039626.5 46156844.0
69 1 46156845.0 46156843.0
70 1 46156844.0 46234129.5
71 1 46234130.5 46234128.5
72 1 46234129.5 46278377.5
73 1 46278378.5 51046373.0
74 1 51046374.0 51350780.0
75 1 51350781.0 51350779.0
76 1 51350780.0 51476967.0
77 1 51476968.0 55024011.0
78 1 55024012.0 55063727.5
79 1 55063728.5 64832651.5
80 1 64832652.5 64967428.0
81 1 64967429.0 71244128.0
82 1 71244129.0 74034013.0
83 1 74034014.0 77943983.0
84 1 77943984.0 77991950.0
85 1 77991951.0 85258900.0
86 1 85258901.0 85298890.5
87 1 85298891.5 92431445.5
88 1 92431446.5 92498535.5
89 1 92498536.5 92498534.5
90 1 92498535.5 92812163.5
91 1 92812164.5 92812162.5
92 1 92812163.5 92842545.5
93 1 92842546.5 97076218.0
94 1 97076219.0 98291224.5
95 1 98291225.5 110310904.0
96 1 110310905.0 110354604.0
97 1 110354605.0 113813561.5
98 1 113813562.5 113876252.5
99 1 113876253.5 113876251.5
100 1 113876252.5 113897023.0
101 1 113897024.0 113897022.0
102 1 113897023.0 113901367.5
103 1 113901368.5 114275579.5
104 1 114275580.5 114539472.0
105 1 114539473.0 114708185.0
106 1 114708186.0 114717046.0
107 1 114717047.0 117134254.0
108 1 117134255.0 117170937.5
109 1 117170938.5 117170936.5
110 1 117170937.5 117573923.5
111 1 117573924.5 117573922.5
112 1 117573923.5 117747171.0
113 1 117747172.0 119417418.0
114 1 119417419.0 119568388.5
115 1 119568389.5 122026458.0
116 1 122026459.0 124932724.0
117 1 124932725.0 147453504.0
118 1 147453505.0 147634146.0
119 1 147634147.0 150344636.5
120 1 150344637.5 150403292.5
121 1 150403293.5 150568840.0
122 1 150568841.0 150604184.0
123 1 150604185.0 150604183.0
124 1 150604184.0 150810078.0
125 1 150810079.0 150810077.0
126 1 150810078.0 150885282.0
127 1 150885283.0 152133720.5
128 1 152133721.5 152157171.5
129 1 152157172.5 152910148.5
130 1 152910149.5 153103992.0
131 1 153103993.0 154167497.5
132 1 154167498.5 154195615.5
133 1 154195616.5 154195614.5
134 1 154195615.5 154271687.0
135 1 154271688.0 154271686.0
136 1 154271687.0 154299362.0
137 1 154299363.0 154299361.0
138 1 154299362.0 154376074.0
139 1 154376075.0 154376073.0
140 1 154376074.0 154467779.5
141 1 154467780.5 155184911.5
142 1 155184912.5 155194335.0
143 1 155194336.0 155305490.0
144 1 155305491.0 155320644.0
145 1 155320645.0 155890737.5
146 1 155890738.5 155912394.5
147 1 155912395.5 156098207.0
148 1 156098208.0 156147126.0
149 1 156147127.0 156759948.5
150 1 156759949.5 156803725.5
151 1 156803726.5 156803724.5
152 1 156803725.5 156859683.0
153 1 156859684.0 156859682.0
154 1 156859683.0 156892538.0
155 1 156892539.0 157563859.0
156 1 157563860.0 157638259.5
157 1 157638260.5 161435776.0
158 1 161435777.0 161692328.5
159 1 161692329.5 162675707.0
160 1 162675708.0 162816720.0
161 1 162816721.0 162816719.0
162 1 162816720.0 163957530.5
163 1 163957531.5 163957529.5
164 1 163957530.5 164866870.5
165 1 164866871.5 170608733.0
166 1 170608734.0 170840734.5
167 1 170840735.5 175979390.5
168 1 175979391.5 176381549.0
169 1 176381550.0 179101293.0
170 1 179101294.0 179265912.5
171 1 179265913.5 188543146.0
172 1 188543147.0 191306996.5
173 1 191306997.5 193113738.0
174 1 193113739.0 193251086.5
175 1 193251087.5 201345848.0
176 1 201345849.0 201377467.5
177 1 201377468.5 202007737.0
178 1 202007738.0 202069037.0
179 1 202069038.0 202325446.5
180 1 202325447.5 202342197.0
181 1 202342198.0 205608410.5
182 1 205608411.5 205691329.5
183 1 205691330.5 206467081.0
184 1 206467082.0 206501829.5
185 1 206501830.5 206501828.5
186 1 206501829.5 206750556.5
187 1 206750557.5 206750555.5
188 1 206750556.5 206772593.0
189 1 206772594.0 228419832.0
190 1 228419833.0 228493443.5
191 1 228493444.5 231359647.5
192 1 231359648.5 231421919.5
193 1 231421920.5 241298169.0
194 1 241298170.0 241525907.0
195 1 241525908.0 243487777.0
196 1 243487778.0 243948408.0
197 1 243948409.0 Inf
198 2 -Inf 3566815.0
199 2 3566816.0 3591889.0
200 2 3591890.0 15941166.0
201 2 15941167.0 16249473.5
202 2 16249474.5 17752990.5
203 2 17752991.5 17799208.0
204 2 17799209.0 24028112.0
205 2 24028113.0 24046567.0
206 2 24046568.0 24493301.0
207 2 24493302.0 24779325.0
208 2 24779326.0 25199410.5
209 2 25199411.5 25345573.5
210 2 25345574.5 25345572.5
211 2 25345573.5 25697255.0
212 2 25697256.0 25697254.0
213 2 25697255.0 25903518.5
214 2 25903519.5 26782183.0
215 2 26782184.0 26845800.5
216 2 26845801.5 36831765.0
217 2 36831766.0 36973918.5
218 2 36973919.5 38069939.0
219 2 38069940.0 38075455.0
220 2 38075456.0 39150279.0
221 2 39150280.0 39239941.5
222 2 39239942.5 42113549.0
223 2 42113550.0 42332831.0
224 2 42332832.0 46336284.0
225 2 46336285.0 46432518.5
226 2 46432519.5 60656621.5
227 2 60656622.5 60839399.5
228 2 60839400.5 60839398.5
229 2 60839399.5 60932339.0
230 2 60932340.0 61474666.5
231 2 61474667.5 61679994.5
232 2 61679995.5 73972554.0
233 2 73972555.0 74135437.5
234 2 74135438.5 88803823.5
235 2 88803824.5 92188144.0
236 2 92188145.0 92188144.0
237 2 92188145.0 94090557.0
238 2 94090558.0 96253630.0
239 2 96253631.0 96265591.5
240 2 96265592.5 96331937.5
241 2 96331938.5 96435717.0
242 2 96435718.0 98459176.0
243 2 98459177.0 98588759.0
244 2 98588760.0 99516742.5
245 2 99516743.5 100058442.0
246 2 100058443.0 108723510.0
247 2 108723511.0 108785264.5
248 2 108785265.5 111123148.0
249 2 111123149.0 111582587.5
250 2 111582588.5 113217908.0
251 2 113217909.0 113278544.5
252 2 113278545.5 127232545.5
253 2 127232546.5 127298674.0
254 2 127298675.0 136050085.0
255 2 136050086.0 136500062.0
256 2 136500063.0 144159110.0
257 2 144159111.0 146154616.0
258 2 146154617.0 146154615.0
259 2 146154616.0 147931344.0
260 2 147931345.0 157737316.0
261 2 157737317.0 157808855.0
262 2 157808856.0 167912540.5
263 2 167912541.5 168351898.0
264 2 168351899.0 172530928.0
265 2 172530929.0 172665848.5
266 2 172665849.5 174799827.5
267 2 174799828.5 174974789.5
268 2 174974790.5 176091339.0
269 2 176091340.0 176097203.5
270 2 176097204.5 176097202.5
271 2 176097203.5 176107179.5
272 2 176107180.5 176107178.5
273 2 176107179.5 176112899.5
274 2 176112900.5 177223592.5
275 2 177223593.5 177328580.0
276 2 177328581.0 189783633.5
277 2 189783634.5 189967216.5
278 2 189967217.5 191021869.0
279 2 191021870.0 191197952.5
280 2 191197953.5 201245807.0
281 2 201245808.0 201289048.0
282 2 201289049.0 203600829.5
283 2 203600830.5 203904672.5
284 2 203904673.5 207579316.5
285 2 207579317.5 208210248.0
286 2 208210249.0 208210247.0
287 2 208210248.0 208267120.5
288 2 208267121.5 211031364.0
289 2 211031365.0 212366117.0
290 2 212366118.0 231988189.5
291 2 231988190.5 232361126.0
292 2 232361127.0 233759715.5
293 2 233759716.5 233772614.0
294 2 233772615.0 236543786.0
295 2 236543787.0 236833644.0
296 2 236833645.0 237817152.0
297 2 237817153.0 237828317.5
298 2 237828318.5 241833838.0
299 2 241833839.0 241864210.0
300 2 241864211.0 241864209.0
301 2 241864210.0 241900314.0
302 2 241900315.0 Inf
303 3 -Inf 10102660.0
304 3 10102661.0 10133911.5
305 3 10133912.5 10133910.5
306 3 10133911.5 10163839.5
307 3 10163840.5 12269428.5
308 3 12269429.5 12452413.5
309 3 12452414.5 12452412.5
310 3 12452413.5 12584164.0
311 3 12584165.0 12584163.0
312 3 12584164.0 12641297.0
313 3 12641298.0 13450178.5
314 3 13450179.5 13502973.0
315 3 13502974.0 14124853.0
316 3 14124854.0 14141855.0
317 3 14141856.0 14141854.0
318 3 14141855.0 14144095.0
319 3 14144096.0 14144094.0
320 3 14144095.0 14178591.0
321 3 14178592.0 30606615.0
322 3 30606616.0 30691951.5
323 3 30691952.5 32922382.0
324 3 32922383.0 32957800.5
325 3 32957801.5 36992936.0
326 3 36992937.0 37052229.0
327 3 37052230.0 38137710.5
328 3 38137711.5 38153158.0
329 3 38153159.0 38483580.5
330 3 38483581.5 38549702.0
331 3 38549703.0 40497069.0
332 3 40497070.0 40521225.5
333 3 40521226.5 40521224.5
334 3 40521225.5 40878352.0
335 3 40878353.0 40878351.0
336 3 40878352.0 41239445.5
337 3 41239446.5 46845870.0
338 3 46845871.0 46872099.0
339 3 46872100.0 49876215.5
340 3 49876216.5 49904457.0
341 3 49904458.0 50223549.0
342 3 50223550.0 50263765.0
343 3 50263766.0 52400842.5
344 3 52400843.5 52411282.0
345 3 52411283.0 60003234.5
346 3 60003235.5 61049517.5
347 3 61049518.5 69562660.0
348 3 69562661.0 69965912.5
349 3 69965913.5 69965911.5
350 3 69965912.5 70958643.0
351 3 70958644.0 70958642.0
352 3 70958643.0 71441400.0
353 3 71441401.0 71441399.0
354 3 71441400.0 72081246.5
355 3 72081247.5 72081245.5
356 3 72081246.5 72875154.5
357 3 72875155.5 88787421.0
358 3 88787422.0 90772457.0
359 3 90772458.0 90772457.0
360 3 90772458.0 93655574.0
361 3 93655575.0 100704325.0
362 3 100704326.0 100749418.0
363 3 100749419.0 105615358.0
364 3 105615359.0 106623409.5
365 3 106623410.5 114265367.5
366 3 114265368.5 114323509.5
367 3 114323510.5 119822027.0
368 3 119822028.0 120130138.5
369 3 120130139.5 122181624.5
370 3 122181625.5 122285192.0
371 3 122285193.0 122794342.5
372 3 122794343.5 122894654.0
373 3 122894655.0 124733098.0
374 3 124733099.0 124744048.5
375 3 124744049.5 124744047.5
376 3 124744048.5 124970871.5
377 3 124970872.5 124970870.5
378 3 124970871.5 125013508.0
379 3 125013509.0 128480777.5
380 3 128480778.5 128720081.5
381 3 128720082.5 134904973.0
382 3 134904974.0 135630340.0
383 3 135630341.0 138644109.0
384 3 138644110.0 138946929.0
385 3 138946930.0 149509713.0
386 3 149509714.0 149703885.0
387 3 149703886.0 155870131.5
388 3 155870132.5 156024971.0
389 3 156024972.0 158543756.0
390 3 158543757.0 158625740.5
391 3 158625741.5 168589953.0
392 3 168589954.0 169766198.5
393 3 169766199.5 170202110.5
394 3 170202111.5 170328768.5
395 3 170328769.5 176414635.5
396 3 176414636.5 177943553.5
397 3 177943554.5 177943552.5
398 3 177943553.5 179196947.5
399 3 179196948.5 179196946.5
400 3 179196947.5 179242486.0
401 3 179242487.0 182942692.5
402 3 182942693.5 182997839.0
403 3 182997840.0 183460050.5
404 3 183460051.5 183602932.0
405 3 183602933.0 184372219.5
406 3 184372220.5 184379309.0
407 3 184379310.0 185067387.5
408 3 185067388.5 185172535.5
409 3 185172536.5 185172534.5
410 3 185172535.5 185269720.5
411 3 185269721.5 185269719.5
412 3 185269720.5 185488436.5
413 3 185488437.5 185993162.5
414 3 185993163.5 186127835.5
415 3 186127836.5 186763599.0
416 3 186763600.0 186789492.5
417 3 186789493.5 187710429.0
418 3 187710430.0 189032588.0
419 3 189032589.0 189032587.0
420 3 189032588.0 189631317.5
421 3 189631318.5 189631316.5
422 3 189631317.5 189894867.5
423 3 189894868.5 195979842.5
424 3 195979843.5 196137628.5
425 3 196137629.5 Inf
426 4 -Inf 1769381.0
427 4 1769382.0 1810751.0
428 4 1810752.0 1810750.0
429 4 1810751.0 1874843.5
430 4 1874844.5 24309638.5
431 4 24309639.5 24691959.5
432 4 24691960.5 25540277.0
433 4 25540278.0 25716705.5
434 4 25716706.5 40125132.5
435 4 40125133.5 40289751.0
436 4 40289752.0 41745579.5
437 4 41745580.5 41843957.5
438 4 41843958.5 49712060.0
439 4 49712061.0 51743951.0
440 4 51743952.0 53371698.5
441 4 53371699.5 53460425.5
442 4 53460426.5 53460424.5
443 4 53460425.5 54167973.5
444 4 54167974.5 54295395.0
445 4 54295396.0 54477608.5
446 4 54477609.5 54477607.5
447 4 54477608.5 54738515.0
448 4 54738516.0 56468599.5
449 4 56468600.5 56493294.0
450 4 56493295.0 64866563.5
451 4 64866564.5 66580872.0
452 4 66580873.0 70993656.5
453 4 70993657.5 71132859.0
454 4 71132860.0 71132858.0
455 4 71132859.0 71568543.0
456 4 71568544.0 71568542.0
457 4 71568543.0 71656539.0
458 4 71656540.0 80235083.5
459 4 80235084.5 80311291.5
460 4 80311292.5 83459622.0
461 4 83459623.0 83529365.0
462 4 83529366.0 86819889.0
463 4 86819890.0 86919935.5
464 4 86919936.5 86919934.5
465 4 86919935.5 87149520.0
466 4 87149521.0 98243039.0
467 4 98243040.0 98457235.5
468 4 98457236.5 98457234.5
469 4 98457235.5 98887072.5
470 4 98887073.5 98887071.5
471 4 98887072.5 98962377.5
472 4 98962378.5 104840909.0
473 4 104840910.0 105322988.5
474 4 105322989.5 108041693.5
475 4 108041694.5 108455072.5
476 4 108455073.5 109891655.0
477 4 109891656.0 110031370.5
478 4 110031371.5 122450568.0
479 4 122450569.0 122522271.5
480 4 122522272.5 122522270.5
481 4 122522271.5 122785534.0
482 4 122785535.0 122785533.0
483 4 122785534.0 122892470.0
484 4 122892471.0 152041790.0
485 4 152041791.0 152527310.0
486 4 152527311.0 153669550.0
487 4 153669551.0 153707685.5
488 4 153707686.5 184303119.0
489 4 184303120.0 184529117.0
490 4 184529118.0 187356320.5
491 4 187356321.5 188147097.0
492 4 188147098.0 Inf
493 5 -Inf 92203.0
494 5 92204.0 212880.5
495 5 212881.5 3600254.0
496 5 3600255.0 5195908.5
497 5 5195909.5 7868376.5
498 5 7868377.5 7899988.5
499 5 7899989.5 31362200.5
500 5 31362201.5 31530470.0
501 5 31530471.0 35832278.0
502 5 35832279.0 35876463.5
503 5 35876464.5 38480870.0
504 5 38480871.0 38562602.5
505 5 38562603.5 38562601.5
506 5 38562602.5 38937677.5
507 5 38937678.5 44003754.5
508 5 44003755.5 44598742.0
509 5 44598743.0 44598741.0
510 5 44598742.0 46485899.0
511 5 46485900.0 46485899.0
512 5 46485900.0 50059807.0
513 5 50059808.0 55932464.5
514 5 55932465.5 56038149.0
515 5 56038150.0 56038148.0
516 5 56038149.0 56793591.0
517 5 56793592.0 56793590.0
518 5 56793591.0 56901880.5
519 5 56901881.5 56901879.5
520 5 56901880.5 57968409.0
521 5 57968410.0 57968408.0
522 5 57968409.0 58477206.5
523 5 58477207.5 67711562.0
524 5 67711563.0 68695781.0
525 5 68695782.0 80654138.0
526 5 80654139.0 80918195.0
527 5 80918196.0 122285422.0
528 5 122285423.0 122619371.5
529 5 122619372.5 132877451.5
530 5 132877452.5 132948842.0
531 5 132948843.0 138279957.0
532 5 138279958.0 138339635.5
533 5 138339636.5 138455664.5
534 5 138455665.5 138488236.5
535 5 138488237.5 138488235.5
536 5 138488236.5 138678529.5
537 5 138678530.5 138678528.5
538 5 138678529.5 138850313.5
539 5 138850314.5 138850312.5
540 5 138850313.5 138877900.5
541 5 138877901.5 138877899.5
542 5 138877900.5 138940454.0
543 5 138940455.0 139474342.0
544 5 139474343.0 139540893.5
545 5 139540894.5 149438384.5
546 5 149438385.5 149551399.0
547 5 149551400.0 150402040.5
548 5 150402041.5 150428522.0
549 5 150428523.0 157071096.5
550 5 157071097.5 157123776.5
551 5 157123777.5 157123775.5
552 5 157123776.5 157173372.5
553 5 157173373.5 157173371.5
554 5 157173372.5 157253013.5
555 5 157253014.5 158278952.5
556 5 158278953.5 159151339.0
557 5 159151340.0 159151338.0
558 5 159151339.0 160058019.0
559 5 160058020.0 160058018.0
560 5 160058019.0 160159089.5
561 5 160159090.5 161616275.5
562 5 161616276.5 161774501.0
563 5 161774502.0 177510733.5
564 5 177510734.5 177519405.5
565 5 177519406.5 Inf
566 6 -Inf 393056.0
567 6 393057.0 447013.5
568 6 447014.5 447012.5
569 6 447013.5 1312313.0
570 6 1312314.0 1312312.0
571 6 1312313.0 1351806.5
572 6 1351807.5 3046804.0
573 6 3046805.0 3116223.0
574 6 3116224.0 14047646.5
575 6 14047647.5 14723319.0
576 6 14723320.0 18121677.0
577 6 18121678.0 18153838.5
578 6 18153839.5 18153837.5
579 6 18153838.5 18223759.0
580 6 18223760.0 18223758.0
581 6 18223759.0 18331639.0
582 6 18331640.0 18331638.0
583 6 18331639.0 20472002.0
584 6 20472003.0 20472001.0
585 6 20472002.0 20518325.5
586 6 20518326.5 26018895.0
587 6 26018896.0 26071887.5
588 6 26071888.5 26071886.5
589 6 26071887.5 26115732.5
590 6 26115733.5 26115731.5
591 6 26115732.5 26279233.5
592 6 26279234.5 26865396.0
593 6 26865397.0 27194156.0
594 6 27194157.0 27194155.0
595 6 27194156.0 27641104.0
596 6 27641105.0 27641103.0
597 6 27641104.0 27900944.5
598 6 27900945.5 28739866.5
599 6 28739867.5 28959323.5
600 6 28959324.5 29700343.0
601 6 29700344.0 29945722.0
602 6 29945723.0 30418121.0
603 6 30418122.0 30519291.5
604 6 30519292.5 30519290.5
605 6 30519291.5 30569890.0
606 6 30569891.0 30569889.0
607 6 30569890.0 30596124.5
608 6 30596125.5 30695604.5
609 6 30695605.5 30717712.5
610 6 30717713.5 31575422.5
611 6 31575423.5 31578144.5
612 6 31578145.5 31736287.5
613 6 31736288.5 31762687.5
614 6 31762688.5 32256218.5
615 6 32256219.5 32422440.5
616 6 32422441.5 32422439.5
617 6 32422440.5 32819520.5
618 6 32819521.5 32897166.0
619 6 32897167.0 32962269.0
620 6 32962270.0 32962268.0
621 6 32962269.0 32993719.5
622 6 32993720.5 32993718.5
623 6 32993719.5 33139964.0
624 6 33139965.0 33317587.5
625 6 33317588.5 33325891.0
626 6 33325892.0 34198843.5
627 6 34198844.5 34423807.5
628 6 34423808.5 35439064.5
629 6 35439065.5 35466323.5
630 6 35466324.5 36561215.5
631 6 36561216.5 36694940.0
632 6 36694941.0 37099075.5
633 6 37099076.5 37193145.0
634 6 37193146.0 41668910.0
635 6 41668911.0 41736888.5
636 6 41736889.5 41934055.0
637 6 41934056.0 41996454.0
638 6 41996455.0 43579259.5
639 6 43579260.5 43615540.0
640 6 43615541.0 43615539.0
641 6 43615540.0 43770304.5
642 6 43770305.5 43770303.5
643 6 43770304.5 43789542.0
644 6 43789543.0 44258236.5
645 6 44258237.5 44269285.5
646 6 44269286.5 58553887.0
647 6 58553888.0 59829934.0
648 6 59829935.0 89022059.5
649 6 89022060.5 89091276.5
650 6 89091277.5 103398951.0
651 6 103398952.0 104898309.0
652 6 104898310.0 104898308.0
653 6 104898309.0 105724776.0
654 6 105724777.0 111631396.5
655 6 111631397.5 112072095.0
656 6 112072096.0 113900616.0
657 6 113900617.0 114014004.0
658 6 114014005.0 117454033.0
659 6 117454034.0 117555739.5
660 6 117555740.5 117555738.5
661 6 117555739.5 118194977.0
662 6 118194978.0 126729678.5
663 6 126729679.5 127238807.0
664 6 127238808.0 134111274.0
665 6 134111275.0 134617854.5
666 6 134617855.5 134617853.5
667 6 134617854.5 135144364.0
668 6 135144365.0 135144363.0
669 6 135144364.0 135251284.0
670 6 135251285.0 136257969.5
671 6 136257970.5 136309889.0
672 6 136309890.0 137178136.5
673 6 137178137.5 137356275.0
674 6 137356276.0 137356274.0
675 6 137356275.0 137776056.0
676 6 137776057.0 137776055.0
677 6 137776056.0 137986655.0
678 6 137986656.0 138802950.0
679 6 138802951.0 138904941.0
680 6 138904942.0 149650004.0
681 6 149650005.0 149723198.0
682 6 149723199.0 151359383.5
683 6 151359384.5 151389280.5
684 6 151389281.5 151389279.5
685 6 151389280.5 151718925.0
686 6 151718926.0 151718924.0
687 6 151718925.0 152099058.5
688 6 152099059.5 158765655.0
689 6 158765656.0 158845772.0
690 6 158845773.0 159476855.5
691 6 159476856.5 159731697.5
692 6 159731698.5 161126690.0
693 6 161126691.0 161349788.0
694 6 161349789.0 161349787.0
695 6 161349788.0 162727896.5
696 6 162727897.5 162727895.5
697 6 162727896.5 163364962.0
698 6 163364963.0 163364961.0
699 6 163364962.0 163641508.5
700 6 163641509.5 166956302.0
701 6 166956303.0 167088123.0
702 6 167088124.0 167088122.0
703 6 167088123.0 167584157.5
704 6 167584158.5 167584156.5
705 6 167584157.5 168109509.5
706 6 168109510.5 Inf
707 7 -Inf 5871271.0
708 7 5871272.0 6004227.5
709 7 6004228.5 13274173.5
710 7 13274174.5 13988756.5
711 7 13988757.5 26187961.5
712 7 26187962.5 26201714.0
713 7 26201715.0 27159206.5
714 7 27159207.5 27221418.0
715 7 27221419.0 27221417.0
716 7 27221418.0 27830662.0
717 7 27830663.0 27830661.0
718 7 27830662.0 28141151.5
719 7 28141152.5 37902153.0
720 7 37902154.0 37918627.5
721 7 37918628.5 37918626.5
722 7 37918627.5 38237667.5
723 7 38237668.5 38237666.5
724 7 38237667.5 38357730.0
725 7 38357731.0 41274929.5
726 7 41274930.5 41702741.5
727 7 41702742.5 50318735.0
728 7 50318736.0 50422844.0
729 7 50422845.0 58169652.0
730 7 58169653.0 61528020.0
731 7 61528021.0 79794165.0
732 7 79794166.0 80672313.5
733 7 80672314.5 86644226.0
734 7 86644227.0 86877953.5
735 7 86877954.5 97794217.0
736 7 97794218.0 98003173.0
737 7 98003174.0 99638975.5
738 7 99638976.5 99679943.0
739 7 99679944.0 102276498.0
740 7 102276499.0 102284041.5
741 7 102284042.5 105520164.5
742 7 105520165.5 105568309.5
743 7 105568310.5 106764009.0
744 7 106764010.0 106975125.5
745 7 106975126.5 107762204.5
746 7 107762205.5 107843733.0
747 7 107843734.0 116683995.5
748 7 116683996.5 116796169.0
749 7 116796170.0 116796168.0
750 7 116796169.0 117479653.5
751 7 117479654.5 124764123.5
752 7 124764124.5 124805828.0
753 7 124805829.0 124805827.0
754 7 124805828.0 125712559.5
755 7 125712560.5 127634069.5
756 7 127634070.5 127999426.0
757 7 127999427.0 127999425.0
758 7 127999426.0 128052326.5
759 7 128052327.5 128052325.5
760 7 128052326.5 128166957.5
761 7 128166958.5 129178412.5
762 7 129178413.5 129296881.0
763 7 129296882.0 137862881.0
764 7 137862882.0 137941750.5
765 7 137941751.5 137941749.5
766 7 137941750.5 138288796.0
767 7 138288797.0 138288795.0
768 7 138288796.0 138589706.5
769 7 138589707.5 139365732.0
770 7 139365733.0 139437790.0
771 7 139437791.0 140724003.5
772 7 140724004.5 140967443.0
773 7 140967444.0 142276644.0
774 7 142276645.0 142532731.5
775 7 142532732.5 142532730.5
776 7 142532731.5 142617434.0
777 7 142617435.0 142617433.0
778 7 142617434.0 142769448.5
779 7 142769449.5 142769447.5
780 7 142769448.5 142790651.5
781 7 142790652.5 142790650.5
782 7 142790651.5 142838554.5
783 7 142838555.5 142939948.5
784 7 142939949.5 142994102.0
785 7 142994103.0 143354020.5
786 7 143354021.5 143370220.5
787 7 143370221.5 148803448.5
788 7 148803449.5 148865624.0
789 7 148865625.0 150902944.5
790 7 150902945.5 150960732.5
791 7 150960733.5 151455161.5
792 7 151455162.5 151876732.5
793 7 151876733.5 151876731.5
794 7 151876732.5 152129132.5
795 7 152129133.5 Inf
796 8 -Inf 11640646.5
797 8 11640647.5 11758567.5
798 8 11758568.5 23201256.5
799 8 23201257.5 23258369.0
800 8 23258370.0 23258368.0
801 8 23258369.0 23287987.0
802 8 23287988.0 23287986.0
803 8 23287987.0 23626467.0
804 8 23626468.0 23626466.0
805 8 23626467.0 23692599.0
806 8 23692600.0 26168221.0
807 8 26168222.0 26376702.5
808 8 26376703.5 37315794.5
809 8 37315795.5 37718175.5
810 8 37718176.5 37718174.5
811 8 37718175.5 37781033.0
812 8 37781034.0 37781032.0
813 8 37781033.0 37843288.5
814 8 37843289.5 38144863.0
815 8 38144864.0 38272330.0
816 8 38272331.0 38272329.0
817 8 38272330.0 38370262.5
818 8 38370263.5 38370261.5
819 8 38370262.5 38412022.0
820 8 38412023.0 38412021.0
821 8 38412022.0 38464476.0
822 8 38464477.0 39875472.0
823 8 39875473.0 39938578.5
824 8 39938579.5 42101740.5
825 8 42101741.5 42232182.0
826 8 42232183.0 42232181.0
827 8 42232182.0 42334962.0
828 8 42334963.0 42892377.0
829 8 42892378.0 43043200.5
830 8 43043201.5 44033743.0
831 8 44033744.0 45877265.0
832 8 45877266.0 45877265.0
833 8 45877266.0 47755961.5
834 8 47755962.5 53964225.5
835 8 53964226.5 54031474.5
836 8 54031475.5 54031473.5
837 8 54031474.5 54302711.5
838 8 54302712.5 54302710.5
839 8 54302711.5 54468569.0
840 8 54468570.0 55910891.5
841 8 55910892.5 56039873.0
842 8 56039874.0 56039872.0
843 8 56039873.0 56139889.0
844 8 56139890.0 56139888.0
845 8 56139889.0 56259352.0
846 8 56259353.0 70091519.5
847 8 70091520.5 70579041.5
848 8 70579042.5 76922981.5
849 8 76922982.5 79714939.5
850 8 79714940.5 79714938.5
851 8 79714939.5 79843227.5
852 8 79843228.5 89930298.0
853 8 89930299.0 89992950.0
854 8 89992951.0 91677584.0
855 8 91677585.0 92618589.0
856 8 92618590.0 107699118.5
857 8 107699119.5 108355889.5
858 8 108355890.5 116813442.5
859 8 116813443.5 116902367.0
860 8 116902368.0 116902366.0
861 8 116902367.0 117665101.5
862 8 117665102.5 117665100.5
863 8 117665101.5 118111226.0
864 8 118111227.0 124463472.0
865 8 124463473.0 124499844.0
866 8 124499845.0 127146223.0
867 8 127146224.0 128744720.0
868 8 128744721.0 132112649.5
869 8 132112650.5 132127542.0
870 8 132127543.0 133238597.5
871 8 133238598.5 133380824.0
872 8 133380825.0 144511132.0
873 8 144511133.0 144518662.0
874 8 144518663.0 Inf
875 9 -Inf 5007132.0
876 9 5007133.0 5102264.0
877 9 5102265.0 5102263.0
878 9 5102264.0 5446011.5
879 9 5446012.5 5446010.5
880 9 5446011.5 5680847.0
881 9 5680848.0 13667890.0
882 9 13667891.0 14575408.5
883 9 14575409.5 15462567.5
884 9 15462568.5 15517298.5
885 9 15517299.5 20066460.0
886 9 20066461.0 20668737.5
887 9 20668738.5 21641984.5
888 9 21641985.5 22053680.5
889 9 22053681.5 27109335.0
890 9 27109336.0 27229231.5
891 9 27229232.5 35073861.5
892 9 35073862.5 35084223.0
893 9 35084224.0 36758792.5
894 9 36758793.5 37023521.5
895 9 37023522.5 43389634.0
896 9 43389635.0 45518558.0
897 9 45518559.0 83962706.5
898 9 83962707.5 83989539.5
899 9 83989540.5 83989538.5
900 9 83989539.5 84505602.5
901 9 84505603.5 84505601.5
902 9 84505602.5 85284131.0
903 9 85284132.0 90728776.5
904 9 90728777.5 91054829.0
905 9 91054830.0 92409772.5
906 9 92409773.5 92437284.5
907 9 92437285.5 95101251.0
908 9 95101252.0 95346017.5
909 9 95346018.5 95346016.5
910 9 95346017.5 95446265.0
911 9 95446266.0 97673208.5
912 9 97673209.5 97775465.0
913 9 97775466.0 98802105.0
914 9 98802106.0 98896436.0
915 9 98896437.0 99069113.0
916 9 99069114.0 99149519.5
917 9 99149520.5 99149518.5
918 9 99149519.5 99524605.5
919 9 99524606.5 99524604.5
920 9 99524605.5 99922000.0
921 9 99922001.0 107407594.0
922 9 107407595.0 108171866.5
923 9 108171867.5 125146464.5
924 9 125146465.5 125195032.5
925 9 125195033.5 127815419.5
926 9 127815420.5 127861243.5
927 9 127861244.5 129884996.0
928 9 129884997.0 130063195.0
929 9 130063196.0 130713921.5
930 9 130713922.5 130889521.0
931 9 130889522.0 132895787.5
932 9 132895788.5 132957671.5
933 9 132957672.5 132957670.5
934 9 132957671.5 133077358.0
935 9 133077359.0 133077357.0
936 9 133077358.0 133151220.5
937 9 133151221.5 134030119.0
938 9 134030120.0 134096619.5
939 9 134096620.5 134096618.5
940 9 134096619.5 134355054.0
941 9 134355055.0 134355053.0
942 9 134355054.0 134539185.0
943 9 134539186.0 136898578.5
944 9 136898579.5 136933360.5
945 9 136933361.5 Inf
The stderror is
Error in throw.default("INTERNAL ERROR: Detected overlapping gaps on chromosome ", :Dec 18 2023, 4:05 PM
INTERNAL ERROR: Detected overlapping gaps on chromosome 10 in argument 'gaps'.
Calls: runAbsoluteCN ... gapsToSegments.data.frame -> throw -> throw.default
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
Session Info
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0
The text was updated successfully, but these errors were encountered: