Closed moldach closed 4 years ago
@moldach would you be able to pull out the row from the vcf that errored along with its mate and paste it here? From just this error message it looks like the break1_orientation is missing but I can't tell more without the data itself
I have been getting the same error
My config
[reference] template_metadata = /reference_inputs/cytoBand.txt masking = /reference_inputs/hg19_masking.tab annotations = /reference_inputs/ensembl69_hg19_annotations.json aligner_reference =/reference_inputs/Genomes/Human_genome/hg19.fa dgv_annotation = /reference_inputs/reference_inputs/dgv_hg19_variants.tab reference_genome = /reference_inputs/Genomes/Human_genome/hg19.fa
[S14N] library = S14N protocol = genome bam_file = /home/ram.nanduri/SV_VCFS/Bam/S14N.recaled.bam read_length = None median_fragment_size = None stdev_fragment_size = None strand_specific = False strand_determining_read = 2 disease_status = normal inputs = manta
[S14T] library = S14T protocol = genome bam_file = /home/ram.nanduri/SV_VCFS/Bam/S14T.recaled.bam read_length = None median_fragment_size = None stdev_fragment_size = None strand_specific = False strand_determining_read = 2 disease_status = diseased inputs = manta [convert] assume_no_untemplated = True manta = convert_tool_output /home/ram.nanduri/SV_VCFS/S14N_vs_S14T/results/variants/diploidSV.vcf.gz /home/ram.nanduri/SV_VCFS/S14N_vs_S14T/results/variants/somaticSV.vcf.gz manta False
My Log MAVIS: 2.2.6 hostname: 10.1.11.37 [2020-06-30 01:19:19] arguments command = 'setup' config = '/home/ram.nanduri/SV_VCFS/MAVIS_ORI_TEST/S14N_vs_S14T.mavis.cfg' log = 'S14N_vs_S14T.Run.log' log_level = 'INFO' output = 'S14N_vs_S14T.mavis.output/' skip_stage = [ 'cluster' 'validate' ] creating output directory: 'S14N_vs_S14T.mavis.output/converted_inputs' setting up the directory structure for S14N as /home/ram.nanduri/SV_VCFS/MAVIS_ORI_TEST/S14N_vs_S14T.mavis.output/S14N_normal_genome converting input command: ['convert_tool_output', '/home/ram.nanduri/SV_VCFS/S14N_vs_S14T/results/variants/diploidSV.vcf.gz', '/home/ram.nanduri/SV_VCFS/S14N_vs_S14T/results/variants/somaticSV.vcf.gz', 'manta', False] reading: /home/ram.nanduri/SV_VCFS/S14N_vs_S14T/results/variants/diploidSV.vcf.gz found 290 rows Error in converting row {'id': 'MantaBND:207:0:1:0:0:0:0', 'break2_orientation': 'R', 'untemplated_seq': 'GCCCCAT', 'break1_chromosome': 'chr1', 'break2_chromosome': 'chr1', 'break1_position_start': 17051724, 'break1_position_end': 17051724, 'break2_position_start': 234912188, 'break2_position_end': 234912188, 'event_type': 'BND', 'MATEID': 'MantaBND:207:0:1:0:0:0:1', 'SVINSLEN': 7, 'SVINSSEQ': 'GCCCCAT', 'BND_DEPTH': 5, 'MATE_BND_DEPTH': 4}
Mate Pairs from the diploidSV.vcf.gz
chr1 17051724 MantaBND:207:0:1:0:0:0:0 C [chr1:234912188[GCCCCATC 36 PASS SVTYPE=BND;MATEID=MantaBND:207:0:1:0:0:0:1;SVINSLEN=7;SVINSSEQ=GCCCCAT;BND_DEPTH=5;MATE_BND_DEPTH=4 GT:FT:GQ:PL:PR:SR 0/1:PASS:30:86,0,28:1,2:3,1
chr1 234912188 MantaBND:207:0:1:0:0:0:1 A [chr1:17051724[ATGGGGCA 36 PASS SVTYPE=BND;MATEID=MantaBND:207:0:1:0:0:0:0;SVINSLEN=7;SVINSSEQ=ATGGGGC;BND_DEPTH=4;MATE_BND_DEPTH=5 GT:FT:GQ:PL:PR:SR 0/1:PASS:30:86,0,28:1,2:3,1
thanks @ramsainanduri! That's really helpful :) I will look into this now
Hi @creisle, Is this bug fixed and when can we expect the new version?
It is fixed and will be released in 2.2.7 which should be released today or in the next couple of days. In the mean time you can build from the fix branch here https://github.com/bcgsc/mavis/tree/bugfix/issue-213-bnd-non-trans if you like
okay thank you.
This has now been released. https://pypi.org/project/mavis/2.2.7/ Please let me know if you have further issues
This works great, thank you!
The
mavis config
steps creates amavis.cfg
for the MAVIS standard input file formats (.bam
and.vcf
); however, according to the the documents the Reference Input Files should be set up using Environment Variables or entered in themavis.cfg
file manually.Set up mavis.cfg
Manually include references
This is how my directory looks like
So I'll add the required references to
mavis.cfg
:Running MAVIS
I'm getting the following error: