isoseq3 collapse stops with fatal error map::at

[jchariker]

Operating system Linux computer cluster

Package name isoseq3 v3.8.2

Conda environment

_libgcc_mutex             0.1                        main
_openmp_mutex             5.1                       1_gnu
avro-python3              1.9.0                    py37_0    bioconda
blas                      1.0                         mkl
brotlipy                  0.7.0           py311h5eee18b_1002
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.19.0               h5eee18b_0
ca-certificates           2023.01.10           h06a4308_0
certifi                   2023.5.7        py311h06a4308_0
cffi                      1.15.1          py311h5eee18b_3
charset-normalizer        2.0.4              pyhd3eb1b0_0
cryptography              39.0.1          py311h9ce1e76_0
htslib                    1.12                 h9093b5e_1    bioconda
idna                      3.4             py311h06a4308_0
intel-openmp              2023.1.0         hdb19cb5_46305
iso8601                   1.0.2              pyhd3eb1b0_0
isoseq3                   3.8.2                h9ee0642_0    bioconda
krb5                      1.19.4               h568e23c_0
ld_impl_linux-64          2.38                 h1181459_1
libcurl                   7.88.1               h91b91d3_0
libdeflate                1.17                 h5eee18b_0
libedit                   3.1.20221030         h5eee18b_0
libev                     4.33                 h7f8727e_1
libffi                    3.4.4                h6a678d5_0
libgcc-ng                 11.2.0               h1234567_1
libgomp                   11.2.0               h1234567_1
libnghttp2                1.46.0               hce63b2e_0
libssh2                   1.10.0               h8f2d780_0
libstdcxx-ng              11.2.0               h1234567_1
libuuid                   1.41.5               h5eee18b_0
lima                      2.7.1                h9ee0642_0    bioconda
mkl                       2023.1.0         h6d00ec8_46342
mkl-service               2.4.0           py311h5eee18b_1
mkl_fft                   1.3.6           py311ha02d727_1
mkl_random                1.2.2           py311ha02d727_1
ncurses                   6.4                  h6a678d5_0
numpy                     1.24.3          py311h08b1b3b_1
numpy-base                1.24.3          py311hf175353_1
openssl                   1.1.1t               h7f8727e_0
pbaa                      1.0.3                hdfd78af_0    bioconda
pbbam                     1.7.0                h058f120_1    bioconda
pbccs                     6.4.0                h9ee0642_0    bioconda
pbcommand                 2.1.1                    py38_0    bioconda
pbcopper                  2.0.0                ha04c180_0    bioconda
pbfusion                  0.1.0                hdfd78af_0    bioconda
pbmarkdup                 1.0.3                h9ee0642_0    bioconda
pbmm2                     1.10.0               h9ee0642_0    bioconda
pbpigeon                  1.0.0                hdfd78af_0    bioconda
pbskera                   0.1.0                hdfd78af_0    bioconda
pbsv                      2.9.0                h9ee0642_0    bioconda
pbtk                      3.1.0                h9ee0642_0    bioconda
pip                       23.0.1          py311h06a4308_0
pycparser                 2.21               pyhd3eb1b0_0
pyopenssl                 23.0.0          py311h06a4308_0
pysocks                   1.7.1           py311h06a4308_0
python                    3.11.3               h7a1cb2a_0
pytz                      2022.7          py311h06a4308_0
readline                  8.2                  h5eee18b_0
recalladapters            9.0.0                h9ee0642_1    bioconda
requests                  2.29.0          py311h06a4308_0
setuptools                66.0.0          py311h06a4308_0
sqlite                    3.41.2               h5eee18b_0
tbb                       2021.8.0             hdb19cb5_0
tk                        8.6.12               h1ccaba5_0
trgt                      0.4.0                hdfd78af_0    bioconda
tzdata                    2023c                h04d1e81_0
urllib3                   1.26.15         py311h06a4308_0
wheel                     0.38.4          py311h06a4308_0
xz                        5.2.10               h5eee18b_1
zlib                      1.2.13               h5eee18b_0

Describe the bug isoseq3 collapse stops with fatal error

Error message

|> 20240509 15:34:22.354 -|- FATAL -|- Run -|- 0x7fb928983900|| -|- isoseq collapse ERROR: map::at

To Reproduce I can give you test.bam (a subset of the original file) which produces the error with the following command: isoseq3 collapse test.bam test_collapse.gff

Expected behavior No error and collapsed file output.

Any help you can provide is much appreciated.

[armintoepfer]

Please provide a minimal reproducible example.

[armintoepfer]

I'll reopen once you've provided a way to reproduce

[jchariker]

Hi Armin, We corrected the problem by upgrading from version 3 to version 4. Julia

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---

From: Armin Töpfer @.> Sent: Thursday, June 27, 2024 10:31:34 AM To: PacificBiosciences/pbbioconda @.> Cc: Chariker, Julia @.>; Author @.> Subject: Re: [PacificBiosciences/pbbioconda] isoseq3 collapse stops with fatal error map::at (Issue #686)

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