search

PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
253 stars 45 forks source link

pbsv call ERROR: Unknown file type for input number 0 with file name #439

Closed amv33576 closed 3 years ago

amv33576 commented 3 years ago

Operating system Linux

Package name pbsv 2.6.2

Conda environment

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge bamtools 2.5.1 h9a82719_9 bioconda biopython 1.79 py38h497a2fe_0 conda-forge brotlipy 0.7.0 py38h497a2fe_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.2 h7f98852_0 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge certifi 2021.10.8 py38h578d9bd_0 conda-forge cffi 1.14.6 py38ha65f79e_0 conda-forge chardet 4.0.0 py38h578d9bd_1 conda-forge charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge conda 4.10.3 py38h578d9bd_2 conda-forge conda-package-handling 1.7.3 py38h497a2fe_0 conda-forge cryptography 35.0.0 py38ha5dfef3_0 conda-forge csvtk 0.23.0 h9ee0642_0 bioconda deprecated 1.2.13 pyh6c4a22f_0 conda-forge freetype 2.10.4 h0708190_1 conda-forge htslib 1.12 h9093b5e_1 bioconda idna 3.1 pyhd3deb0d_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jpeg 9d h36c2ea0_0 conda-forge krb5 1.19.2 hcc1bbae_2 conda-forge last 1238 h2e03b76_0 bioconda lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge ldc 1.20.0 h9a1ace1_1 conda-forge lerc 2.2.1 h9c3ff4c_0 conda-forge libblas 3.9.0 12_linux64_openblas conda-forge libcblas 3.9.0 12_linux64_openblas conda-forge libcurl 7.79.1 h2574ce0_1 conda-forge libdeflate 1.7 h7f98852_5 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 11.2.0 h1d223b6_11 conda-forge libgfortran-ng 11.2.0 h69a702a_11 conda-forge libgfortran5 11.2.0 h5c6108e_11 conda-forge libgomp 11.2.0 h1d223b6_11 conda-forge liblapack 3.9.0 12_linux64_openblas conda-forge libnghttp2 1.43.0 h812cca2_1 conda-forge libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libssh2 1.10.0 ha56f1ee_2 conda-forge libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge libtiff 4.3.0 hf544144_1 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libzlib 1.2.11 h36c2ea0_1013 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge nanofilt 2.8.0 py_0 bioconda nanoget 1.16.1 py_0 bioconda nanomath 1.2.1 pyhdfd78af_0 bioconda nanosv 1.2.4 py_0 bioconda ncurses 6.2 h58526e2_4 conda-forge numpy 1.21.2 py38he2449b9_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openssl 1.1.1l h7f98852_0 conda-forge pandas 1.3.3 py38h43a58ef_0 conda-forge parallel 20210822 ha770c72_0 conda-forge pbmm2 1.7.0 hdcc8f71_0 bioconda pbsv 2.6.2 h9ee0642_0 bioconda perl 5.32.1 1_h7f98852_perl5 conda-forge pillow 8.3.2 py38h8e6f84c_0 conda-forge porechop 0.2.4 pypi_0 pypi pycosat 0.6.3 py38h497a2fe_1006 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge pysam 0.17.0 py38hf7546f9_0 bioconda pysocks 1.7.1 py38h578d9bd_3 conda-forge python 3.8.5 h7579374_1
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.8 2_cp38 conda-forge pytz 2021.3 pyhd8ed1ab_0 conda-forge pyvcf 0.6.8 py38h32f6830_1002 conda-forge readline 8.1 h46c0cb4_0 conda-forge requests 2.26.0 pyhd8ed1ab_0 conda-forge ruamel_yaml 0.15.80 py38h497a2fe_1004 conda-forge sambamba 0.8.1 h41abebc_0 bioconda seqkit 2.0.0 h9ee0642_0 bioconda seqtk 1.3 h5bf99c6_3 bioconda setuptools 58.2.0 py38h578d9bd_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.36.0 h9cd32fc_2 conda-forge tabix 1.11 hdfd78af_0 bioconda tk 8.6.11 h27826a3_1 conda-forge tqdm 4.62.3 pyhd8ed1ab_0 conda-forge urllib3 1.26.7 pyhd8ed1ab_0 conda-forge wrapt 1.13.2 py38h497a2fe_0 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zlib 1.2.11 h36c2ea0_1013 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge

Describe the bug pbsv call did not work.

sequence of commands: pbmm2 align scaffold1.mmi reads.ccs.fastq scaffold1.pbmm2.sr.bam --preset CCS --sort -j 16 -J 8 --rg '@RG\tID:myid\tSM:scaffold1' -> This worked, I can see the alignments

pbsv discover scaffold1.pbmm2.sr.bam scaffold1.pbmm2.svsig.gz --> Run, not error message

pbsv call --ccs scaffold1.fas scaffold1.pbmm2.svsig.gz scaffold1.pbmm2.vcf --> it did not run.

Error message >|> 20211016 05:51:57.299 -|- FATAL -|- Run at ../subprojects/pbcopper/src/cli2/CLI.cpp:139 -|- 0x7f61115cd780|| -|- pbsv call ERROR: Unknown file type for input number 0 with file name "scaffold1.fas"

To Reproduce I am aligning the reads to one scaffold of a butterfly genome.

Expected behavior Call structural variants from structural variant signatures.

armintoepfer commented 3 years ago

There's no support for .fas, rename it to .fasta