TypeError: __init__() got multiple values for argument 'name'
moldach opened this issue · 4 comments
moldach commented
I'm getting an unknown error when trying to run svviz2 on a shared-academic HPC. I believe that I have all the dependencies installed referenced in PATH.
Load modules/environment
module load nixpkgs/16.09
module load trf/4.09
module load scipy-stack
module load bwa/0.7.17
module load gcc/7.3.0
module load r/3.6.1
pip install rpy2
pip install -U git+git://github.com/nspies/svviz2.git
Run svviz2
ssw library not found
2020-03-18 22:36:54 - svviz2.app.sample - INFO - Loaded pre-computed read statistics for N2_trim_bwaMEM_sort_dedupped
2020-03-18 22:36:54 - svviz2.app.main - INFO - Search distance: 614bp
2020-03-18 22:36:54 - svviz2.app.main - INFO - Align distance: 847bp
[W::vcf_parse] Contig 'I' is not defined in the header. (Quick workaround: index the file with tabix.)
2020-03-18 22:36:54 - svviz2.io.vcfparser - WARNING - Only tandem duplications are supported; if this duplication is in fact a tandem duplication, make sure that the alt field of the vcf record is '<DUP:TANDEM>': I 4341001 N2_CNVnator_dup_1 N<DUP> . PASS END=4357000;SVTYPE=DUP;SVLEN=16000;IMPRECISE;natorRD=2.36251;natorP1=1.53711e-06;natorP2=0;natorP3=3.93758e-05;natorP4=0;natorQ0=0.977525
2020-03-18 22:36:54 - svviz2.io.vcfparser - WARNING - Only tandem duplications are supported; if this duplication is in fact a tandem duplication, make sure that the alt field of the vcf record is '<DUP:TANDEM>': I 10204001 N2_CNVnator_dup_2 N <DUP> . PASS END=10220000;SVTYPE=DUP;SVLEN=16000;IMPRECISE;natorRD=8.14429;natorP1=0.00274125;natorP2=0;natorP3=0.0209727;natorP4=0;natorQ0=0.829033
[W::vcf_parse] Contig 'III' is not defined in the header. (Quick workaround: index the file with tabix.)
2020-03-18 22:36:54 - svviz2.io.vcfparser - WARNING - Only tandem duplications are supported; if this duplication is in fact a tandem duplication, make sure that the alt field of the vcf record is '<DUP:TANDEM>': III 8334001 N2_CNVnator_dup_3 N<DUP> . PASS END=8353000;SVTYPE=DUP;SVLEN=19000;IMPRECISE;natorRD=1.96942;natorP1=0.0166545;natorP2=1.18954e+09;natorP3=0.016989;natorP4=1.30514e+09;natorQ0=0.84234
[W::vcf_parse] Contig 'IV' is not defined in the header. (Quick workaround: index the file with tabix.)
))))DEL: Deletion::IV:4,921,000-4,927,999(7000)
2020-03-18 22:36:54 - svviz2.app.datahub - INFO - Working on variant 0: Deletion::IV:4,921,000-4,927,999(7000)
2020-03-18 22:36:54 - svviz2.app.datahub - INFO - Looking for existing realignments; will try to open a few bam files that may not yet exist...
[E::hts_open_format] Failed to open file /scratch/moldach/data/calls/svviz2-tempxb9wa3f4/N2_CNVnator_del_4.del_IV_4921000.N2_trim_bwaMEM_sort_dedupped.alt.sorted.bam
2020-03-18 22:36:54 - svviz2.app.datahub - INFO - Analyzing sample N2_trim_bwaMEM_sort_dedupped
2020-03-18 22:36:54 - svviz2.io.getreads - INFO - Loading more read pairs...
2020-03-18 22:36:54 - svviz2.io.getreads - INFO - TIME to read batch: 0.0s
2020-03-18 22:36:54 - svviz2.app.datahub - INFO - Analyzing 288 read pairs
2020-03-18 22:36:54 - svviz2.app.genomesource - INFO - Loading bwa index from file ../references/c_elegans.PRJNA13758.WS274.genomic.fa...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
2020-03-18 22:36:54 - svviz2.app.genomesource - INFO - Loading bwa index done.
100%|█████████████████████████████████████████████| 288/288 [00:03<00:00, 84.06it/s]
Reads with only N: 0
REF: 10.95 ALT: 0
TIME::: 4.215909004211426
Traceback (most recent call last):
File "/scratch/moldach/bin/svviz2-env/bin/svviz2", line 11, in <module>
load_entry_point('svviz2==2.0a3', 'console_scripts', 'svviz2')()
File "/scratch/moldach/bin/svviz2-env/lib/python3.7/site-packages/svviz2/app/main.py", line 60, in main
run(datahub)
File "/scratch/moldach/bin/svviz2-env/lib/python3.7/site-packages/svviz2/app/main.py", line 46, in run
visualize.visualize(datahub)
File "/scratch/moldach/bin/svviz2-env/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 58, in visualize
_visualize(datahub)
File "/scratch/moldach/bin/svviz2-env/lib/python3.7/site-packages/svviz2/visualize/visualize.py", line 76, in _visualize
genome_view = GenomeView(part.id, start, end, "+", source, name=part.id)
TypeError: __init__() got multiple values for argument 'name'
Hope this helps. Let me know if you need any more information and I'll see what I can get.
nspies commented
I think you're using a very old version of GenomeView. Can you try updating?
pip install --upgrade genomeview
moldach commented
I have version 0.9.1 which seems to be the most up-to-date version:
(svviz2) [moldach@cedar5 svviz2]$ pip install --upgrade genomeview
Ignoring pip: markers 'python_version < "3"' don't match your environment
Looking in links: /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/avx2, /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic
Requirement already up-to-date: genomeview in /home/moldach/svviz2/lib/python3.7/site-packages (0.9.1)
nspies commented
Ah, that's it -- you need genomeview >= 1.0. https://pypi.org/project/genomeview/1.0.1/ is the latest released version as of June 25, 2018.
Looks like you're using some non-standard pypi repository.
moldach commented
Bringing in the newer version of genomeview via pip install genomeview==1.0.1 causes this error:
ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview:
pip install --upgrade --force-reinstall genomeview
If I try to run pip install --upgrade --force-reinstall genomeview it forces genomeview back to version 0.9.0. Waiting to hear from IT staff at ComputeCanada as to why/if pip is pulling from a non-standard pypi repo.