Open byb121 opened 4 years ago
When using GRCh38 as the reference, some of our samples suffered the error below:
[Tue Sep 17 20:14:22 2019] Beginning TopHat-Fusion post-processing run (v2.1.0) ----------------------------------------------- [Tue Sep 17 20:14:22 2019] Extracting 23-mer around fusions and mapping them using Bowtie [Tue Sep 17 20:14:26 2019] Filtering fusions Processing: tophat_PR7519a.1/fusions.out Processing: tophat_PR7519a.10/fusions.out Processing: tophat_PR7519a.11/fusions.out Processing: tophat_PR7519a.12/fusions.out Processing: tophat_PR7519a.13/fusions.out Ignoring: malformed coordinates:[ HLA-B*57:11:3016 ] Ignoring: malformed coordinates:[ HLA-B*57:01:01:3016 ] Ignoring: malformed coordinates:[ HLA-B*57:06:2963 ] Ignoring: malformed coordinates:[ HLA-B*57:29:3016 ] Processing: tophat_PR7519a.14/fusions.out Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:03:2499 ] Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:01:2499 ] Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:02:2498 ] Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:03:2499 ] Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:01:2499 ] Ignoring: malformed coordinates:[ HLA-DQB1*03:01:01:02:2498 ] Processing: tophat_PR7519a.15/fusions.out Processing: tophat_PR7519a.16/fusions.out Processing: tophat_PR7519a.2/fusions.out Processing: tophat_PR7519a.3/fusions.out Processing: tophat_PR7519a.4/fusions.out Traceback (most recent call last): File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 2927, in <module> sys.exit(main()) File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 2898, in main filter_fusion(bwt_idx_prefix, params) File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 998, in filter_fusion filter_fusion_impl(fusion_file, junctions, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list) File "/software/CGP/canpipe/live/bin/tophat-fusion-post", line 804, in filter_fusion_impl chr, coord = chr_coord.split(':') ValueError: too many values to unpack Command exited with non-zero status 1
When using GRCh38 as the reference, some of our samples suffered the error below: