pairtools
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open2c
Warning when running with pysam 0.23.1 leading to non-zero exit code
I encounter the following warning when running pairtools with pysam 0.23.1:
> conda create -n pairtools pairtools
...
The following packages will be downloaded:
package | build
---------------------------|-----------------
biopython-1.85 | py312h66e93f0_1 3.3 MB conda-forge
brotli-python-1.1.0 | py312h2ec8cdc_2 342 KB conda-forge
cffi-1.17.1 | py312h06ac9bb_0 288 KB conda-forge
contourpy-1.3.2 | py312h68727a3_0 270 KB conda-forge
cytoolz-1.0.1 | py312h66e93f0_0 385 KB conda-forge
fonttools-4.58.1 | py312h178313f_0 2.7 MB conda-forge
kiwisolver-1.4.8 | py312h84d6215_0 70 KB conda-forge
matplotlib-base-3.10.3 | py312hd3ec401_0 7.8 MB conda-forge
numpy-1.26.4 | py312heda63a1_0 7.1 MB conda-forge
pairix-0.3.9 | py312h4711d71_0 101 KB bioconda
pairtools-1.1.3 | py312h5219090_0 357 KB bioconda
pandas-2.2.3 | py312hf9745cd_3 14.7 MB conda-forge
pillow-11.2.1 | py312h80c1187_0 40.5 MB conda-forge
pysam-0.23.1 | py312h47d5410_0 4.6 MB bioconda
python-3.12.10 |h9e4cc4f_0_cpython 29.8 MB conda-forge
python_abi-3.12 | 7_cp312 7 KB conda-forge
pyyaml-6.0.2 | py312h178313f_2 202 KB conda-forge
scipy-1.15.2 | py312ha707e6e_0 16.3 MB conda-forge
unicodedata2-16.0.0 | py312h66e93f0_0 395 KB conda-forge
zstandard-0.23.0 | py312h66e93f0_2 715 KB conda-forge
------------------------------------------------------------
Total: 130.0 MB
...
> conda activate pairtools
> pairtools
<frozen importlib._bootstrap>:228: RuntimeWarning: pysam.libcalignedsegment.AlignedSegment size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
Usage: pairtools [OPTIONS] COMMAND [ARGS]...
Flexible tools for Hi-C data processing.
All pairtools have a few common options, which should be typed _before_ the
command name.
Options:
--post-mortem Post mortem debugging
--output-profile TEXT Profile performance with Python cProfile and dump the
statistics into a binary file
-v, --verbose Verbose logging.
-d, --debug On error, drop into the post-mortem debugger shell.
--version Show the version and exit.
-h, --help Show this message and exit.
Commands:
dedup Find and remove PCR/optical duplicates.
filterbycov Remove pairs from regions of high coverage.
flip Flip pairs to get an upper-triangular matrix.
header Manipulate the .pairs/.pairsam header
markasdup Tag all pairs in the input file as duplicates.
merge Merge .pairs/.pairsam files.
parse Find ligation pairs in .sam data, make .pairs.
parse2 Extracts pairs from .sam/.bam data with complex walks,...
phase Phase pairs mapped to a diploid genome.
restrict Assign restriction fragments to pairs.
sample Select a random subset of pairs in a pairs file.
scaling Calculate pairs scalings.
select Select pairs according to some condition.
sort Sort a .pairs/.pairsam file.
split Split a .pairsam file into .pairs and .sam.
stats Calculate pairs statistics.
This exits with exit code 2.
Manually downgrading to pysam 0.23.0 fixes the issue and pairtools runs as expected.
Pysam has inadvertently created a binary compatibility problem. Most packages using pysam are pure Python themselves, so concerns like this are immaterial. However some, like pairtools, are Cython projects and should be able to assume some binary compatibility guarantees from pysam.
The pysam maintainers will make a 0.23.2 release soon that fixes this issue.
Pysam 0.23.2 has now been released and removes this warning.
(pairtools with no arguments exits with status 2 regardless. pairtools --help would exit with status 0.)