segfault on loading chromosome

[hexylena]

Hi, I'm really excited to try this out but I'm experiencing a segfault on my system. It crashes as soon as I load the genome, and I'm not sure why.

Here's my current script:

import gwplot

print(gwplot.__file__)

# Initialise with reference genome
gw = gwplot.Gw("./hg38.fasta")
print(gw)

#gw.add_region("chr12", 49018978, 49060794)
#gw.save_png("output.png")

I've tried with both ./hg38.fasta and hg38. Both crash:

$ pixi run python3.12 test.py
/home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/__init__.py
Fontconfig error: Cannot load default config file: No such file: (null)
Fontconfig error: Cannot load default config file: No such file: (null)
Fontconfig error: Cannot load default config file: No such file: (null)
$ echo $?
1

pixi.toml

[workspace]
authors = ["Helena Rasche <hexylena@galaxians.org>"]
channels = ["conda-forge"]
name = "gwplot"
platforms = ["linux-64"]
version = "0.1.0"

[tasks]

[dependencies]
python = "3.12.*"

[pypi-dependencies]
gwplot = ">=0.4.1, <0.5"

backtrace

[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `/home/user/kg/gwplot/.pixi/envs/default/bin/python3.12 test.py'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x0000792c6cf11be0 in SkTypeface::getFamilyName(SkString*) const () from /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/../gwplot.libs/libgw-859e37e0.so
[Current thread is 1 (Thread 0x792c6e835580 (LWP 3839485))]
Missing file(s), try: dnf --enablerepo='*debug*' install /usr/lib/.build-id/22/e3510fb5dd0f867643dec5e9a1910b80097c22 /usr/lib/debug/.build-id/22/e3510fb5dd0f867643dec5e9a1910b80097c22.debug
(gdb) bt
#0  0x0000792c6cf11be0 in SkTypeface::getFamilyName(SkString*) const () from /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/../gwplot.libs/libgw-859e37e0.so
#1  0x0000792c6ccf08f0 in Themes::Fonts::setTypeface (this=this@entry=0x62c4aefbf1c0, fontStr="Menlo", size=14) at src/themes.cpp:1230
#2  0x0000792c6cd81a2c in Manager::GwPlot::GwPlot (this=0x62c4aefb8190, reference="./hg38.fasta", bampaths=std::vector of length 0, capacity 0, opt=..., regions=..., 
    track_paths=std::vector of length 0, capacity 0) at src/plot_manager.cpp:84
#3  0x0000792c642c3624 in __pyx_pf_6gwplot_9interface_2Gw___cinit__(__pyx_obj_6gwplot_9interface_Gw*, _object*, _object*) [clone .constprop.0] ()
   from /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/interface.cpython-312-x86_64-linux-gnu.so
#4  0x0000792c642c4277 in __pyx_tp_new_6gwplot_9interface_Gw(_typeobject*, _object*, _object*) ()
   from /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/interface.cpython-312-x86_64-linux-gnu.so
#5  0x000062c4979ce063 in type_call (kwds=0x0, args=0x792c6e7d4820, type=0x792c64d628a0 <__pyx_type_6gwplot_9interface_Gw>) at /usr/local/src/conda/python-3.12.11/Objects/typeobject.c:1667
#6  _PyObject_MakeTpCall (tstate=0x62c497e57910 <_PyRuntime+458992>, callable=0x792c64d628a0 <__pyx_type_6gwplot_9interface_Gw>, args=0x792c6eb2a078, nargs=<optimized out>, keywords=0x0)
    at /usr/local/src/conda/python-3.12.11/Objects/call.c:240
#7  0x000062c4978e1b23 in _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=0x792c6eb2a020, throwflag=<optimized out>) at Python/bytecodes.c:2715
#8  0x000062c497a7f1a1 in PyEval_EvalCode (co=co@entry=0x792c6e7a4ae0, globals=globals@entry=0x792c6e7d1900, locals=locals@entry=0x792c6e7d1900)
    at /usr/local/src/conda/python-3.12.11/Python/ceval.c:580
#9  0x000062c497ab98ca in run_eval_code_obj (tstate=tstate@entry=0x62c497e57910 <_PyRuntime+458992>, co=co@entry=0x792c6e7a4ae0, globals=globals@entry=0x792c6e7d1900, 
    locals=locals@entry=0x792c6e7d1900) at /usr/local/src/conda/python-3.12.11/Python/pythonrun.c:1757
#10 0x000062c497ab4585 in run_mod (mod=mod@entry=0x62c4aeb6c4c0, filename=filename@entry=0x792c6e578e90, globals=globals@entry=0x792c6e7d1900, locals=locals@entry=0x792c6e7d1900, 
    flags=flags@entry=0x7ffe84112bf0, arena=arena@entry=0x792c6e6f7cb0) at /usr/local/src/conda/python-3.12.11/Python/pythonrun.c:1778
#11 0x000062c497ab1620 in pyrun_file (fp=fp@entry=0x62c4aeaca490, filename=filename@entry=0x792c6e578e90, start=start@entry=257, globals=globals@entry=0x792c6e7d1900, 
    locals=locals@entry=0x792c6e7d1900, closeit=closeit@entry=1, flags=0x7ffe84112bf0) at /usr/local/src/conda/python-3.12.11/Python/pythonrun.c:1674
#12 0x000062c497ab12be in _PyRun_SimpleFileObject (fp=0x62c4aeaca490, filename=0x792c6e578e90, closeit=1, flags=0x7ffe84112bf0)
    at /usr/local/src/conda/python-3.12.11/Python/pythonrun.c:459
#13 0x000062c497ab0fe4 in _PyRun_AnyFileObject (fp=0x62c4aeaca490, filename=filename@entry=0x792c6e578e90, closeit=closeit@entry=1, flags=flags@entry=0x7ffe84112bf0)
    at /usr/local/src/conda/python-3.12.11/Python/pythonrun.c:78
#14 0x000062c497aadeb2 in pymain_run_file_obj (skip_source_first_line=0, filename=0x792c6e578e90, program_name=0x792c6e70b630) at /usr/local/src/conda/python-3.12.11/Modules/main.c:361
#15 pymain_run_file (config=0x62c497dfa4f0 <_PyRuntime+77008>) at /usr/local/src/conda/python-3.12.11/Modules/main.c:380
#16 pymain_run_python (exitcode=0x7ffe84112bc4) at /usr/local/src/conda/python-3.12.11/Modules/main.c:634
#17 Py_RunMain () at /usr/local/src/conda/python-3.12.11/Modules/main.c:714
#18 0x000062c497a69247 in Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at /usr/local/src/conda/python-3.12.11/Modules/main.c:768
#19 0x0000792c6e860088 in __libc_start_call_main (main=main@entry=0x62c497a69190 <main>, argc=argc@entry=2, argv=argv@entry=0x7ffe84112e58) at ../sysdeps/nptl/libc_start_call_main.h:58
#20 0x0000792c6e86014b in __libc_start_main_impl (main=0x62c497a69190 <main>, argc=2, argv=0x7ffe84112e58, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, 
    stack_end=0x7ffe84112e48) at ../csu/libc-start.c:360
#21 0x000062c497a690ed in _start ()

coredumpctl

           PID: 3839485 (python3.12)
           UID: 1000 (user)
           GID: 1000 (user)
        Signal: 11 (SEGV)
     Timestamp: Thu 2025-07-03 11:33:57 CEST (2min 31s ago)
  Command Line: /home/user/kg/gwplot/.pixi/envs/default/bin/python3.12 test.py
    Executable: /home/user/kg/gwplot/.pixi/envs/default/bin/python3.12
 Control Group: /user.slice/user-1000.slice/user@1000.service/app.slice/app-org.gnome.Terminal.slice/vte-spawn-ddb12827-a1fb-4238-a4aa-bf6399a91246.scope
          Unit: user@1000.service
     User Unit: vte-spawn-ddb12827-a1fb-4238-a4aa-bf6399a91246.scope
         Slice: user-1000.slice
     Owner UID: 1000 (user)
       Boot ID: 11c030f9e16349febe1fbfc65f46c411
    Machine ID: f62c108da2924d7882ae02dc862266b6
      Hostname: w-lumc
       Storage: /var/lib/systemd/coredump/core.python3\x2e12.1000.11c030f9e16349febe1fbfc65f46c411.3839485.1751535237000000.zst (present)
  Size on Disk: 5.4M
       Message: Process 3839485 (python3.12) of user 1000 dumped core.
                
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                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_ctypes.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libGLdispatch-64b28464.so.0.0.0 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libGLdispatch-64b28464.so.0.0.0
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/binascii.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/binascii.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_json.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_json.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libctabix.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libctabix.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_sha2.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_sha2.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/liblzma.so.5 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/liblzma.so.5
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libcurl-c96f124b.so.4.5.0 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libcurl-c96f124b.so.4.5.0
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libuuid-95b83d40.so.1.3.0 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libuuid-95b83d40.so.1.3.0
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libGLESv2-ed5eda4f.so.2.1.0 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libGLESv2-ed5eda4f.so.2.1.0
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_contextvars.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_random.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_random.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_bisect.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_bisect.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/math.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/math.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_lzma.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_lzma.cpython-312-x86_64-linux-gnu.so
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libexpat.so.1.10.1 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libexpat.so.1.10.1
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libEGL-48f73270.so.1.1.0 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libEGL-48f73270.so.1.1.0
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libbz2.so.1.0.8 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libbz2.so.1.0.8
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libhts-2e7e1711.so.1.21 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libhts-2e7e1711.so.1.21
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcutils.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/.local/lib/python3.12/site-packages/pysam/libcutils.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libfreetype-9c6dd3db.so.6.20.2 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libfreetype-9c6dd3db.so.6.20.2
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libglfw-b10d2d69.so.3.3 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libglfw-b10d2d69.so.3.3
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libgw-859e37e0.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libgw-859e37e0.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libfontconfig-f5cab88b.so.1.12.1 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libfontconfig-f5cab88b.so.1.12.1
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/glfw_interface.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/glfw_interface.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/zlib.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/zlib.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libz.so.1.3.1 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libz.so.1.3.1
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libgcc_s.so.1 without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/libgcc_s.so.1
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_bz2.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/_bz2.cpython-312-x86_64-linux-gnu.so
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/array.cpython-312-x86_64-linux-gnu.so without build-id.
                Module /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/lib-dynload/array.cpython-312-x86_64-linux-gnu.so
                Module libXau.so.6 from rpm libXau-1.0.11-6.fc40.x86_64
                Module libGLdispatch.so.0 from rpm libglvnd-1.7.0-4.fc40.x86_64
                Module libXext.so.6 from rpm libXext-1.3.6-1.fc40.x86_64
                Module libGLX.so.0 from rpm libglvnd-1.7.0-4.fc40.x86_64
                Module libxcb.so.1 from rpm libxcb-1.17.0-2.fc40.x86_64
                Module libGL.so.1 from rpm libglvnd-1.7.0-4.fc40.x86_64
                Module libX11.so.6 from rpm libX11-1.8.10-2.fc40.x86_64
                Stack trace of thread 3839485:
                #0  0x0000792c6cf11be0 n/a (/home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libgw-859e37e0.so + 0x311be0)
                #1  0x0000792c6cd81a2c n/a (/home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot.libs/libgw-859e37e0.so + 0x181a2c)
                #2  0x0000792c642c3624 n/a (/home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/interface.cpython-312-x86_64-linux-gnu.so + 0xc3624)
                #3  0x0000620061747361 n/a (n/a + 0x0)
                ELF object binary architecture: AMD x86-64

I noticed when I checked bt -full that Menlo was being requested

(gdb) bt -full -n 3
#0  0x000073f770911be0 in SkTypeface::getFamilyName(SkString*) const () from /home/user/kg/gwplot/.pixi/envs/default/lib/python3.12/site-packages/gwplot/../gwplot.libs/libgw-859e37e0.so
No symbol table info available.
#1  0x000073f7706f08f0 in Themes::Fonts::setTypeface (this=this@entry=0x5b4d0a1ea1c0, fontStr="Menlo", size=14) at src/themes.cpp:1230
        familyName = {fRec = {fPtr = 0x73f77131ade8 <SkString::gEmptyRec>}, static gEmptyRec = {fLength = 0, fRefCnt = std::atomic<int> = { 0 }, fBeginningOfData = ""}}
        val = <optimized out>
        font_c = <optimized out>
        system_default = false
        fontMgr = {fPtr = 0x5b4d0a080d00}
        face = {fPtr = 0x0}
        ts = <optimized out>

It wasn't available locally, so, I've installed a font with the name Menlo now, but the same error persists. Happy to provide whatever information is useful to debug this :)

[kcleal]

Hi @hexylena,

Thanks for providing a detailed report!

It's a bit unclear, but I think this is being caused by a mismatch between your system fontconfig, and the fontconfig that skia was compiled with. Currently when you build gwplot from source, it downloads a pre-built skia binary (skia is a monster to build). Another user ran into a similar issue using gw kcleal/gw#61 , although I'm not sure if it was resolved.

What system are you using?

gw and gwplot can be configured to use an older version of skia which might get around this issue. If you set OLD_SKIA=1 as an environment variable before you install, then gwplot will download an older version of skia (m93).

Have you tried one of the wheel files available of Pypi, they should bundle their own version of fontconfig? Also, if you have time, could you check to see if gw suffers from the same issue on your machine https://github.com/kcleal/gw (I expect it will!)

Thanks!

[hexylena]

Hi @kcleal

Ahh interesting! It's fedora 40 which I recognise is getting a bit old. I can get a .. similar error on 41.

I cleaned out the environment and try with OLD_SKIA, but I suspect something was cached somewhere, I'll try again later with a fresh cache.

I can confirm that the wheel files on pypi do indeed work! So at least that is sufficient for me, for now :)

I tested building GW from source but that failed on ‘HTS_MOD_REPORT_UNCHECKED’ was not declared in this scope, I'll re-try in a conda/pixi environment soon.

success with wheel

15:56:32 w-lumc:[~/kg/gwplot-pip2]130$ pip install /home/user/Downloads/gwplot-0.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Processing /home/user/Downloads/gwplot-0.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Collecting numpy>=1.19.3 (from gwplot==0.4.1)
  Using cached numpy-2.3.1-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (62 kB)
Collecting pysam>=0.23.0 (from gwplot==0.4.1)
  Using cached pysam-0.23.3-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (1.7 kB)
Using cached numpy-2.3.1-cp312-cp312-manylinux_2_28_x86_64.whl (16.6 MB)
Using cached pysam-0.23.3-cp312-cp312-manylinux_2_28_x86_64.whl (24.0 MB)
Installing collected packages: pysam, numpy, gwplot
Successfully installed gwplot-0.4.1 numpy-2.3.1 pysam-0.23.3

[notice] A new release of pip is available: 23.3.2 -> 25.1.1
[notice] To update, run: pip install --upgrade pip
15:56:39 w-lumc:[~/kg/gwplot-pip2]$ python test.py
/home/user/kg/gwplot-pip2/.direnv/python-3.12/lib64/python3.12/site-packages/gwplot/__init__.py
Fontconfig warning: "/usr/share/fontconfig/conf.avail/05-reset-dirs-sample.conf", line 6: unknown element "reset-dirs"
Gw(reference='<reference>', canvas_width=1366, canvas_height=768, theme='dark', threads=1)
python test.py  7,07s user 0,72s system 93% cpu 8,379 total

[kcleal]

Ok thanks for testing. The HTS error from GW is due to an older version of htslib (system lib), I believe