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bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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Schedule : Stopping submission. Dependencies not complete #226

Closed Nitin123-4 closed 3 years ago

Nitin123-4 commented 3 years ago

[2020-10-11 07:46:02] validate [2020-10-11 07:46:02] annotate [2020-10-11 07:46:04] loading: ['hg38.cytoBand.txt'] [2020-10-11 07:46:04] loading: ['ensembl_human_hg38.87.json'] [2020-10-11 07:50:41] loading: ['hg38.fa'] submitted MA_normal_batch-L8XXsViecS3kgponLaGqAr-1 MA_normal_batch-L8XXsViecS3kgponLaGqAr-1 (kVKgfnLz4EDNWJp7TrGfkS) is SUBMITTED [2020-10-11 08:44:37] pairing Stopping submission. Dependencies not complete MP_batch-L8XXsViecS3kgponLaGqAr is NOT SUBMITTED [2020-10-11 08:44:37] summary MS_batch-L8XXsViecS3kgponLaGqAr is NOT SUBMITTED rewriting: S103744.mavis.output/build.cfg

please help me to resolve this.

Nitin123-4 commented 3 years ago

I think issue is there in annotate step:

(46326789, 'position not found in mapping', dict_keys([Interval(46326809, 46326947), Interval(46326948, 46433189), Interval(46433190, 46433505), Interval(46433506, 46435288), Interval(46435289, 46435396), Interval(46435397, 46447562), Interval(46447563, 46447692), Interval(46447693, 46450295), Interval(46450296, 46450349)])) Traceback (most recent call last): File "mavis/main.py", line 373, in main annotate_main.main(args, start_time=start_time) File "mavis/annotate/main.py", line 254, in main drawing, legend = draw(drawing_config, ann, reference_genome.content, template_metadata.content, drawings_directory) File "mavis/annotate/main.py", line 51, in draw other_settings File "mavis/illustrate/diagram.py", line 222, in draw_sv_summary_diagram reference_genome=reference_genome File "mavis/illustrate/elements.py", line 429, in draw_ustranscript pixel = mapping.convert_ratioed_pos(b.start) | mapping.convert_ratioed_pos(b.end) File "mavis/interval.py", line 488, in convert_ratioed_pos raise IndexError(pos, 'position not found in mapping', self.mapping.keys()) IndexError: (46326789, 'position not found in mapping', dict_keys([Interval(46326809, 46326947), Interval(46326948, 46433189), Interval(46433190, 46433505), Interval(46433506, 46435288), Interval(46435289, 46435396), Interval(46435397, 46447562), Interval(46447563, 46447692), Interval(46447693, 46450295), Interval(46450296, 46450349)]))

Nitin123-4 commented 3 years ago

46326789, 'position not found in mapping' This is giving issues for other samples also. For some samples where I don't have this position in vcf its working all fine.

Sample1:

18 46326721 MantaDEL:249567:0:0:0:0:0 TGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAG T 129 PASS END=46326789;SVTYPE=DEL;SVLEN=-68;CIGAR=1M68D;CIPOS=0,95;HOMLEN=95;HOMSEQ=GAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACC GT:FT:GQ:PL:PR:SR 0/1:PASS:56:179,0,53:6,0:6,6

Sample2:

18 46326721 MantaDEL:314990:0:0:0:0:0 TGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAG T 26 PASS END=46326789;SVTYPE=DEL;SVLEN=-68;CIGAR=1M68D;CIPOS=0,95;HOMLEN=95;HOMSEQ=GAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACCGTCCAAGGAGGGCTTCAGCGGCAGAGGGGAGACC GT:FT:GQ:PL:PR:SR 0/1:PASS:24:76,0,26:3,0:6,3

I am using hg38 genome here. (hg38.87 from Ensembl)

Nitin123-4 commented 3 years ago

Please look into this.

Nitin123-4 commented 3 years ago

Please update if have any solution.

calchoo commented 3 years ago

Hi @Nitin123-4 ,

Can I just confirm what version of mavis you're running?

I'm having difficulties replicating the bug, could you please post more information that is logged around the error and the arguments list?

e.g

[2020-10-14 15:57:56] arguments
                        annotation_filters = 'choose_more_annotated,choose_transcripts_by_priority'
                        annotations = ['/gsc/pipelines/mavis/reference_files/ensembl79_hg38_annotations.json']
                        breakpoint_color = '#000000'
                        command = 'annotate'
                        domain_color = '#ccccb3'
                        domain_mismatch_color = '#b2182b'
...

[2020-10-14 15:57:56] loading: ['/gsc/pipelines/mavis/reference_files/ensembl79_hg38_annotations.json']
[2020-10-14 16:06:03] loading: ['/gsc/pipelines/mavis/reference_files/hg38_reference_genome.fa']
                      (1 of 1) gathering annotations for BPP(Breakpoint(18:46326721-46326816L), Breakpoint(18:46326789R), opposing=False, seq='')
                      generated 1 annotations
                      opening for write: test/annotations.tab
                      opening for write: test/annotations.fusion-cdna.fa
                      (1 of 1) current annotation pLrnqtUcTiEYXQ9hmpVakL-a1 PreTranscript(ENSG00000141622:46326809-46450349, name=ENST00000593230) IntergenicRegion(18:46326789_46326789+) deletion
                      BPP(Breakpoint(18:46326789R), Breakpoint(18:46326809-46326816L), opposing=False, seq='')
ramsainanduri commented 3 years ago 
                  MAVIS: 2.2.6
                  hostname: ##############

[2020-10-11 23:54:08] arguments annotation_filters = 'choose_more_annotated,choose_transcripts_by_priority' annotations = ['ensembl_human_hg38.87.json'] breakpoint_color = '#000000' command = 'annotate' domain_color = '#ccccb3' domain_mismatch_color = '#b2182b' domain_name_regex_filter = '^PF\d+$' domain_scaffold_color = '#000000' draw_fusions_only = False draw_non_synonymous_cdna_only = False drawing_width_iter_increase = 500 exon_min_focus_size = 10 gene1_color = '#657e91' gene1_color_selected = '#518dc5' gene2_color = '#325556' gene2_color_selected = '#4c9677' inputs = ['Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/cluster/batch-mHbxLxUFnjVHxPstPkTdNb-1.tab'] label_color = '#000000' library = 'Test_Sample' log = 'Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/annotate/batch-mHbxLxUFnjVHxPstPkTdNb-1/job-MA_Test_Sample_batch-mHbxLxUFnjVHxPstPkTdNb-1-Nsekcx9gvoCdQwgUk56y8P.log' log_level = 'INFO' mask_fill = '#ffffff' mask_opacity = 0.7 masking = ['hg38_masking.tab'] max_drawing_retries = 5 max_orf_cap = 3 max_proximity = 5000 min_domain_mapping_match = 0.9 min_orf_size = 300 novel_exon_color = '#5D3F6A' output = 'Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/annotate/batch-mHbxLxUFnjVHxPstPkTdNb-1' protocol = 'genome' reference_genome = ['hg38.fa'] scaffold_color = '#000000' splice_color = '#000000' template_metadata = ['hg38.cytoBand.txt'] width = 1000 cached content: ['hg38.cytoBand.txt'] creating output directory: 'Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/annotate/batch-mHbxLxUFnjVHxPstPkTdNb-1/drawings' loading: Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/cluster/batch-mHbxLxUFnjVHxPstPkTdNb-1.tab loaded 4715 breakpoint pairs read 4715 breakpoint pairs cached content: ['ensembl_human_hg38.87.json'] cached content: ['hg38.fa']

                  (2534 of 5666) current annotation bVjnTJsjq6udLpS4yZYoLG-a1 PreTranscript(ENSG00000141622:46326809-46450349, name=ENST00000593230) IntergenicRegion(18:46326789_46326789+) deletion
                  BPP(Breakpoint(18:46326789R), Breakpoint(18:46326809-46326816L), opposing=False, seq='')
                  drawing attempt: 1 1000px
                  closing: Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/annotate/batch-mHbxLxUFnjVHxPstPkTdNb-1/annotations.tab
                  closing: Test_Sample.Manta/results/variants/Test_Sample.mavis.output/Test_Sample_normal_genome/annotate/batch-mHbxLxUFnjVHxPstPkTdNb-1/annotations.fusion-cdna.fa

(46326789, 'position not found in mapping', dict_keys([Interval(46326809, 46326947), Interval(46326948, 46433189), Interval(46433190, 46433505), Interval(46433506, 46435288), Interval(46435289, 46435396), Interval(46435397, 46447562), Interval(46447563, 46447692), Interval(46447693, 46450295), Interval(46450296, 46450349)])) Traceback (most recent call last): File "/home/USER/.local/lib/python3.7/site-packages/mavis/main.py", line 373, in main annotate_main.main(args, start_time=start_time) File "/home/USER/.local/lib/python3.7/site-packages/mavis/annotate/main.py", line 254, in main drawing, legend = draw(drawing_config, ann, reference_genome.content, template_metadata.content, drawings_directory) File "/home/USER/.local/lib/python3.7/site-packages/mavis/annotate/main.py", line 51, in draw other_settings File "/home/USER/.local/lib/python3.7/site-packages/mavis/illustrate/diagram.py", line 222, in draw_sv_summary_diagram reference_genome=reference_genome File "/home/USER/.local/lib/python3.7/site-packages/mavis/illustrate/elements.py", line 429, in draw_ustranscript pixel = mapping.convert_ratioed_pos(b.start) | mapping.convert_ratioed_pos(b.end) File "/home/USER/.local/lib/python3.7/site-packages/mavis/interval.py", line 488, in convert_ratioed_pos raise IndexError(pos, 'position not found in mapping', self.mapping.keys()) IndexError: (46326789, 'position not found in mapping', dict_keys([Interval(46326809, 46326947), Interval(46326948, 46433189), Interval(46433190, 46433505), Interval(46433506, 46435288), Interval(46435289, 46435396), Interval(46435397, 46447562), Interval(46447563, 46447692), Interval(46447693, 46450295), Interval(46450296, 46450349)]))

calchoo commented 3 years ago

Thanks for the logs!

I have a fix for this that should be pushed for release by next week.

In the meantime, to get around this issue you can try run the jobs with these options set to true:

draw_fusions_only = True
draw_non_synonymous_cdna_only = True
creisle commented 3 years ago

v2.2.8 has now been released which includes this fix