Comments (3)
depristo
commented on August 26, 2024
Thanks @machomachopadre for your report. Just so I'm 100% clear, you've got python 2.7 and 3.5 on the machine, and our build-prereqs.sh script is installing some packages into python 3.5 and some into 2.7? I don't think we've been clear before about this, but DeepVariant is intended for python 2.7 only, as we've never tested it using python3.
Can you confirm that you can install DeepVariant on a clean Ubuntu 16 instance in the cloud?
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adhoc-researcher
commented on August 26, 2024
@depristo This might be happening because I'd aliased the "python3" command as "python", which is supposed to be for python 2.7 by default. Any idea as to how I could reset everything such that it installs only for python 2.7 (I've already removed the alias)?
EDIT: The closing and reopening of the issue was a mistake, please ignore.
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depristo
commented on August 26, 2024
Unfortunately I'm not really sure how to do that. It sounds like you've resolved the issue w.r.t. DeepVariant though. I'm closing this bug.
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Related Issues (20)
- ValueError: Reference contigs span 3137161264 bases but only 63025520 bases (2.01%) were found in common among our input files. Check that the sources were created on a common genome reference build. HOT 1
- I read DeepVariant essay and want to download some data. HOT 4
- Error while running tests on Calling variants in non-autosomal contigs HOT 4
- Memory issue while running deepvariant_1.6.0.sif with ONT_R104 HOT 7
- Program always run HOT 3
- DeepVariant running slow HOT 1
- AssertionError: Some objects had attributes which were not restored: HOT 4
- I have a question about training DeepVariant. HOT 2
- Source code compilation of DeepVariant failed HOT 3
- What is deepvariant trained on? HOT 3
- DeepVariant Channel clarification HOT 2
- Info Singularity HOT 1
- dealing with chimeric alignments HOT 3
- Question about RNA-seq HOT 5
- Running with Conda HOT 4
- Checkpoint "Model files do not exist" when testing custom model HOT 1
- make_examples_core.py gets stuck on STAR aligned rnaseq BAM (deepvariant 1.6.1) HOT 1
- No output files (VCFs) for all genome HOT 7
- No output vcf obtained from custom model HOT 1
- [libprotobuf ERROR external/com_google_protobuf/src/google/protobuf/wire_format_lite.cc:584] HOT 2
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