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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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uncaught exception for isoseq cluster2 #658

Closed chenhijy closed 4 months ago

chenhijy commented 4 months ago

Operating system Which operating system and version are you using?

Ubuntu 20.04.6 LTS (GNU/Linux 5.4.0-153-generic x86_64)

Package name Which package / tool is causing the problem? Which version are you using, use tool --version. Have you updated to the latest version conda update package? Have you updated the complete env by running conda update --all? Have you ensured that your channel priorities are set up according to the bioconda recommendations at https://bioconda.github.io/#set-up-channels?

isoseq 4.0.0 (commit v4.0.0)

Using:
  pbbam     : 2.4.99 (commit v2.4.0-16-g5cc6e4b)
  pbcopper  : 2.3.99 (commit v2.3.0-14-g5ac5693)
  pbmm2     : 1.11.99 (commit v1.11.0-1-g1b5a417)
  minimap2  : 2.15
  parasail  : 2.1.3
  boost     : 1.77
  htslib    : 1.17
  zlib      : 1.2.13

Conda environment What is the result of conda list? (Try to paste that between triple backticks.)

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
avro-python3              1.10.2             pyhd8ed1ab_0    conda-forge
biopython                 1.79             py37h540881e_2    conda-forge
brotli-python             1.0.9            py37hd23a5d3_7    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.27.0               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
curl                      8.5.0                hca28451_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
iso8601                   2.1.0              pyhd8ed1ab_0    conda-forge
isoseq                    4.0.0                h9ee0642_0    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libsqlite                 3.45.1               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
numpy                     1.21.6           py37h976b520_0    conda-forge
openssl                   3.2.1                hd590300_0    conda-forge
pbcommand                 2.1.1                      py_2    bioconda
pbcore                    2.1.2                      py_2    bioconda
pbcoretools               0.8.1                      py_1    bioconda
pbfusion                  0.4.0                hdfd78af_0    bioconda
pbmm2                     1.13.1               h9ee0642_0    bioconda
pbsv                      2.9.0                h9ee0642_0    bioconda
pbtk                      3.1.1                h9ee0642_0    bioconda
pip                       24.0               pyhd8ed1ab_0    conda-forge
pysam                     0.16.0           py37ha9a96c6_0    bioconda
pysocks                   1.7.1            py37h89c1867_5    conda-forge
python                    3.7.12          hf930737_100_cpython    conda-forge
python_abi                3.7                     4_cp37m    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
setuptools                69.0.3             pyhd8ed1ab_0    conda-forge
sqlite                    3.45.1               h2c6b66d_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Describe the bug A clear and concise description of what the bug is.

If any of the the input *flnc.bam files are empty (say, from 0 reads passing the requirement of N polyA tails), isoseq cluster2 causes a Segmentation fault (core dumped). Would be nice to handle this exception gracefully.

Error message Paste the error message / stack.

| 20240312 22:19:46.535 | INFO | Effective commandline : cluster2 rootTissues.fofn rootTissues.clustered.bam
| 20240312 22:19:46.535 | INFO | Version               : 4.0.0 (commit v4.0.0)
| 20240312 22:19:46.535 | INFO | Options 
| 20240312 22:19:46.535 | INFO | - CPU threads         : 64
| 20240312 22:19:46.535 | INFO | - Sorting threads     : 64
| 20240312 22:19:46.535 | INFO | - Kmer size           : 17
| 20240312 22:19:46.535 | INFO | - Merge rounds        : 2
| 20240312 22:19:46.535 | INFO | - 5' overhang         : 100
| 20240312 22:19:46.535 | INFO | - 3' overhang         : 30
| 20240312 22:19:46.535 | INFO | - 5' errors           : 5
| 20240312 22:19:46.535 | INFO | - 3' errors           : 10
| 20240312 22:19:46.535 | INFO | - 5' non-match window : 10
| 20240312 22:19:46.535 | INFO | - 3' non-match window : 10
| 20240312 22:19:46.535 | INFO | - Max gaps            : 5
| 20240312 22:19:46.535 | INFO | - Gap window          : 20
| 20240312 22:19:46.535 | INFO | - Max consensus cov   : 50
| 20240312 22:19:46.535 | INFO | - Deduplicate         : True
| 20240312 22:19:46.535 | INFO | - Break clusters      : True
| 20240312 22:19:46.535 | INFO | - Break consensus     : True
| 20240312 22:19:46.535 | INFO | - Output singletons   : False
| 20240312 22:19:46.535 | INFO | - POA intermediate    : False
| 20240312 22:19:46.535 | INFO | - POA final           : True
| 20240312 22:19:46.535 | INFO | - Use QVs for POA     : False
| 20240312 22:19:46.535 | INFO | Temp file name        : /data1/tmp/tmp.1671077.bam
| 20240312 22:19:46.537 | INFO | Get offsets
| 20240312 22:19:46.553 | INFO | Get offsets           : 17ms 439us 
| 20240312 22:19:46.553 | INFO | Consolidate offsets
| 20240312 22:19:46.553 | INFO | Consolidate offsets   : 7us 791ns 
| 20240312 22:19:46.553 | INFO | Sorting
| 20240312 22:19:46.553 | INFO | Sorting               : 5us 933ns 
| 20240312 22:19:46.586 | INFO | Write sorted
| 20240312 22:19:46.590 | INFO | Write sorted          : 37ms 153us 
| 20240312 22:19:46.596 | INFO | Dedup
| 20240312 22:19:46.610 | INFO | Dedup                 : 14ms 584us 
| 20240312 22:19:46.614 | INFO | Clustering
| 20240312 22:19:46.622 | INFO | Clustering            : 7ms 829us 
Segmentation fault (core dumped)
armintoepfer commented 4 months ago

Thank you for your help. I think we've fixed this internally and it will be part of the next release.

armintoepfer commented 4 months ago

I've double checked and this should be fixed in the upcoming release