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ShixiangWang / gcap

GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data and absolute copy number profiles. https://shixiangwang.r-universe.dev/gcap
https://shixiangwang.github.io/gcap/
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Error occured while running GCAP with docker #46

Open CC-DrDU opened 1 month ago

CC-DrDU commented 1 month ago

Hi Shixiang. It me again hahaha.

In the past few days I tried to run GCAP workflow using docker. However, error occured during Step 1. Here is the issue.

2024-07-31 13:02:46.783007 info [gcap.workflow]: ===================== 2024-07-31 13:02:46.861744 info [gcap.workflow]: GCAP WORKFLOW 2024-07-31 13:02:46.874999 info [gcap.workflow]: ===================== 2024-07-31 13:02:46.87687 info [gcap.workflow]: 2024-07-31 13:02:46.878666 info [gcap.workflow]: ===================== 2024-07-31 13:02:46.880441 info [gcap.workflow]: Step 1: Run ASCAT 3.0 2024-07-31 13:02:46.882128 info [gcap.workflow]: ===================== 2024-07-31 13:02:46.916249 info [gcap.runASCAT]: > Run ASCAT on WES data < 2024-07-31 13:02:46.91948 info [gcap.runASCAT]: 2024-07-31 13:02:46.92314 info [gcap.runASCAT]: Configs: 2024-07-31 13:02:46.926549 info [gcap.runASCAT]: result path set to /home/dell/WES_LANDSCAPE_2024/GCAP/test_run_gcap/ 2024-07-31 13:02:46.928997 info [gcap.runASCAT]: allelecounter_exe set to /opt/conda/envs/cancerit/bin/alleleCounter 2024-07-31 13:02:46.931258 info [gcap.runASCAT]: g1000allelesprefix set to /home/dell/WES_LANDSCAPE_2024/GCAP/1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr 2024-07-31 13:02:46.933726 info [gcap.runASCAT]: g1000lociprefix set to /home/dell/WES_LANDSCAPE_2024/GCAP/1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_loci_chrstring_chr 2024-07-31 13:02:46.935469 info [gcap.runASCAT]: GCcontentfile set to /home/dell//WES_LANDSCAPE_2024/GCAP/GC_correction_hg38.txt 2024-07-31 13:02:46.937241 info [gcap.runASCAT]: replictimingfile set to /home/dell/WES_LANDSCAPE_2024/GCAP/RT_correction_hg38.txt 2024-07-31 13:02:46.938991 info [gcap.runASCAT]: nthreads set to 10 2024-07-31 13:02:46.940747 info [gcap.runASCAT]: minCounts set to 10 2024-07-31 13:02:46.942546 info [gcap.runASCAT]: BED_file set to /home/dell/WES_LANDSCAPE_2024/S07604514_Regions.bed 2024-07-31 13:02:46.94439 info [gcap.runASCAT]: probloci_file set to NA 2024-07-31 13:02:46.946275 info [gcap.runASCAT]: chrom_names set to <1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22> 2024-07-31 13:02:46.948128 info [gcap.runASCAT]: gender set to 2024-07-31 13:02:46.949991 info [gcap.runASCAT]: min_base_qual set to 20 2024-07-31 13:02:46.951839 info [gcap.runASCAT]: min_map_qual set to 35 2024-07-31 13:02:46.953615 info [gcap.runASCAT]: penalty set to 70 2024-07-31 13:02:46.956273 info [gcap.runASCAT]: skip_finished_ASCAT set to FALSE 2024-07-31 13:02:46.960423 info [gcap.runASCAT]: 1 jobs detected 2024-07-31 13:02:46.96337 info [FUN]: start submitting job T17 2024-07-31 13:02:46.966261 info [FUN]: tumor data file: T17.bqsr.bam 2024-07-31 13:02:46.968438 info [FUN]: normal data file: 1221.bqsr.bam 2024-07-31 13:02:46.970265 info [FUN]: tumor sample name: T17 2024-07-31 13:02:46.972052 info [FUN]: normal sample name: 1221 Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Reading locis Done reading locis Multi pos start: Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Reading locis Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Reading locis Reading locis Reading locis Done reading locis Multi pos start: Done reading locis Multi pos start: Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Reading locis Done reading locis Multi pos start: Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: Reading locis Done reading locis Multi pos start: [1] Reading Tumor LogR data... [1] Reading Tumor BAF data... [1] Reading Germline LogR data... [1] Reading Germline BAF data... [1] Registering SNP locations... [1] Splitting genome in distinct chunks... 2024-07-31 13:09:39.251546 fatal [value[[3L]]]: job T17 failed in ASCAT due to following error 2024-07-31 13:09:39.28275 info [value[[3L]]]: duplicate row.names: 202201, 234986, 261210, 261972, 266248, 267519, 283190, 294530, 296847, 301442, 320957, 323649, 324170, 338106, 340363, 351265, 357042, 364795, 372700, 372784, 378816, 388922, 391355, 395511, 400220, 408643, 409322, 418601, 435463, 442622, 452738, 454054, 477935, 487979, 492573, 504584, 505006, 531504, 532596, 541737, 558497, 565390, 567196, 568958, 584112, 590316, 595168, 606607, 609081, 612430, 615389, 618675, 632060, 634488, 644168, 649639, 654091, 654229, 666677, 672067, 678561, 679436, 693647, 710763, 711229, 713384, 723197, 727446, 728191, 729033, 729039, 733344, 737030, 737188, 739217, 741912, 744480, 755136, 767078, 771740, 774135, 774982, 780689, 783028, 786660, 788110, 805578, 818986, 822697, 834781, 840319, 869280, 870467, 874501, 883788, 887073, 892135, 907933, 915764, 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5785111, 5804124, 5805654, 5809501, 5821338, 5872618, 5873149, 5874238, 5874866, 5878655, 5882519, 5884227, 5884932, 5885875, 5887748, 5892683, 5904285, 5912983, 5913239, 5913328, 5921914, 5926212, 5938022, 5950470, 5952237, 5961349, 5978905, 5995033, 5996209, 5997991, 6007468, 6013882, 6020952, 6024498, 6027085, 6033248, 6037520, 6051838, 6052295, 6057345, 6057770, 6058176, 60731 2024-07-31 13:09:39.286844 info [value[[3L]]]: ===== 2024-07-31 13:09:39.289119 info [value[[3L]]]: Please check your input bam files (if missing bam index? if its alignment quality is lower?) 2024-07-31 13:09:39.291706 info [value[[3L]]]: ===== I guess there was something wrong with my .bam files, although I have provided the corresponding index file and those .bam files were succesfully used for the usual WES workflow. Anyways, I will try again using R directly, but could you please let if you have any clue about this issue? Thank you and your remarkable work!
ShixiangWang commented 1 month ago

Based on the error, this is probably an issue related to reference files you are using. Please take a deep look at https://github.com/ShixiangWang/gcap?tab=readme-ov-file#install-ascat-required