Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

VCF lossless conversion tests are failing for Zarr 2.11.0

See original GitHub issue

From https://github.com/pystatgen/sgkit/runs/5401218690?check_suite_focus=true (which is truncated due to lots of output):

2022-03-03T15:45:05.4820016Z =========================== short test summary info ============================
2022-03-03T15:45:05.4820284Z FAILED sgkit/tests/io/vcf/test_vcf_lossless_conversion.py::test_lossless_conversion[CEUTrio.20.21.gatk3.4.g.vcf.bgz]
2022-03-03T15:45:05.4820484Z FAILED sgkit/tests/io/vcf/test_vcf_lossless_conversion.py::test_lossless_conversion[all_fields.vcf]
2022-03-03T15:45:05.4820638Z = 2 failed, 813 passed, 32 skipped, 2 xfailed, 1 xpassed in 259.62s (0:04:19) ==

I haven’t been able to reproduce this, but it looks like some fields are nan (e.g. QUAL) which is odd:

2022-03-03T15:45:05.4783854Z #CHROM     POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  s1      s2
2022-03-03T15:45:05.4783952Z 1  1       .       G       A,C     nan     PASS    IB0     .       .       .

Issue Analytics

State:
Created 2 years ago
Comments:6

Top GitHub Comments

1reaction

tomwhitecommented, Mar 10, 2022

Opened https://github.com/pydata/xarray/issues/6347

0reactions

tomwhitecommented, Dec 15, 2022

Fixed in zarr-developers/zarr-python#834

Top Results From Across the Web

Can't set write_empty_chunks in Zarr encoding #6347 - GitHub

Zarr 2.11.0 made a change where chunks with data equal to the fill value are ... VCF lossless conversion tests are failing for...

VCF lossless conversion tests are failing for Zarr 2.11.0 - bytemeta

I looked into this a bit more and found that it's due to changes in Zarr 2.11.0. In that release, chunks with no...

Package List — Spack 0.20.0.dev0 documentation

It creates control-flow models of each MPI process and, when a failure occurs, ... 2.11.1, 2.11.0, 2.10.4, 2.10.3, 2.10.2, 2.10.1, 2.10.0, 2.9.1, 2.9.0, ......

List of supported software - EasyBuild documentation

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for ...

Paquets logiciels dans « focal », Sous-section python - Ubuntu

... standard library test suite for PyPy (an alternative Python interpreter) ... python3-img2pdf (0.3.3-1ubuntu3.1) [universe]: Lossless conversion of ...