nspies
commented
7 years ago Turns out I only tested the functionality outputting the ambiguous alignments when running with --only-realign-locally enabled, so the short-term fix is to use that option.
Closed jzook closed 7 years ago
nspies
commented
7 years ago Turns out I only tested the functionality outputting the ambiguous alignments when running with --only-realign-locally enabled, so the short-term fix is to use that option.
For some of the bams (10X, MP, and 300x illumina), I get an error like this one, where it seems it can't find the amb temp bam file.
(svviz2test343) [jzook@sh-18-30 /scratch/PI/msalit/jzook/AJTrio/svvizconfirm/AJTrio_svviz_random5000_170509]$ genosv --outdir svvizgenosvIllMP --ref /scratch/PI/msalit/jzook/references/human_g1k_v37.fasta -V manualcuration_examples.vcf.gz /scratch/PI/msalit/nspies/data/ajtrio/matepair/HG002.mate_pair.sorted.bam ssw library not found INFO:genosv.io.readstatistics: counts +/-:0 -/+:50001 +/+:0 -/-:0 unpaired:0
load_entry_point('genosv', 'console_scripts', 'genosv')()
File "/home/jzook/svviz2test343/genosv/genosv/app/main.py", line 51, in main
run(datahub)
File "/home/jzook/svviz2test343/genosv/genosv/app/main.py", line 42, in run
report.report(datahub)
File "/home/jzook/svviz2test343/genosv/genosv/app/report.py", line 17, in report
results.extend(tally_nearby_polymorphisms(datahub))
File "/home/jzook/svviz2test343/genosv/genosv/app/report.py", line 186, in tally_nearby_polymorphisms
bam = sample.outbam(allele, "r")
File "/home/jzook/svviz2test343/genosv/genosv/app/sample.py", line 147, in outbam
return pysam.AlignmentFile(self.outbam_paths[allele].replace(".bam", ".sorted.bam"))
File "pysam/libcalignmentfile.pyx", line 401, in pysam.libcalignmentfile.AlignmentFile.cinit (pysam/libcalignmentfile.c:5835)
File "pysam/libcalignmentfile.pyx", line 564, in pysam.libcalignmentfile.AlignmentFile._open (pysam/libcalignmentfile.c:7578)
OSError: file
INFO:genosv.io.readstatistics: insert size mean: 6529.08 std: 1112.71 min:1279(1433) max:11785(8658) INFO:genosv.io.readstatistics: discordant: 0.0636 ALIGNMENT PARAMS::: illumina INFO:genosv.app.main:Search distance: 8,870bp INFO:genosv.app.main:Align distance: 13,080bp ))))DEL: Deletion::5:26,600,716-26,600,835(119) INFO:genosv.app.datahub:Working on Deletion::5:26,600,716-26,600,835(119) INFO:genosv.io.getreads:Loading more read pairs... INFO:genosv.app.datahub:Analyzing 1632 read pairs INFO:genosv.app.genomesource:Loading bwa index from file /scratch/PI/msalit/jzook/references/human_g1k_v37.fasta... [M::bwa_idx_load_from_disk] read 0 ALT contigs INFO:genosv.app.genomesource:Loading bwa index done. 100%|█████████████████████████████████████████████████████████████████████| 1632/1632 [01:19<00:00, 20.49it/s] Reads with only N: 0 REF: 9.1 ALT: 1.0 ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR!ERROR! TIME::: 86.18634986877441 count {'ref': 14, 'alt': 1} mapq {'ref': 12.634442049551081, 'alt': 0.9999} weighted {'ref': 9.1, 'alt': 1.0} Traceback (most recent call last): File "/home/jzook/svviz2test343/bin/genosv", line 11, in
b'svvizgenosvIllMP/genosv-temp/HG2_10X_allpass_922.del_5_26600716.HG002_mate_pair.amb.sorted.bam'not found