armintoepfer
commented
7 months ago You can't use fastq to ubam converted data as input. Please try to get the original unaligned BAM file.
MisoT2901 @.***> schrieb am Mi., 31. Jan. 2024, 01:03:
Operating system 5.14.0-162.6.1.el9_1.x86_64 GNU/Linux
Package name isoseq 4.0.0
Conda environment _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bamtools 2.5.2 hdcf5f25_2 bioconda bedtools 2.31.1 hf5e1c6e_0 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.23.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge htslib 1.17 h6bc39ce_1 bioconda isoseq 4.0.0 h9ee0642_0 bioconda keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.20.1 hf9c8cef_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libcurl 7.87.0 h6312ad2_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lima 2.9.0 h9ee0642_1 bioconda ncurses 6.4 h59595ed_2 conda-forge openssl 1.1.1w hd590300_0 conda-forge pbccs 6.4.0 h9ee0642_0 bioconda pbmm2 1.13.1 h9ee0642_0 bioconda pbpigeon 1.2.0 h4ac6f70_0 bioconda pbskera 1.2.0 hdfd78af_0 bioconda pbtk 3.1.1 h9ee0642_0 bioconda pip 20.1.1 pyh9f0ad1d_0 conda-forge pyfaidx 0.5.3 py27_0 bioconda pysam 0.8.4 py27_0 bioconda python 2.7.15 h5a48372_1011_cpython conda-forge python_abi 2.7 1_cp27mu conda-forge readline 8.2 h8228510_1 conda-forge samtools 1.18 hd87286a_0 bioconda setuptools 44.0.0 py27_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.44.2 h2c6b66d_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge
Describe the bug Hi, I am trying to process some single cells isoseq data, which the ccs reads were in fastq.gz. I managed to covert the fastq.gz to unaligned bam file. I have followed the the standard single cells isoseq pipeline ( https://isoseq.how/umi/examples.html) till the isoseq groupdedup step, which I encounter the following error:
isoseq groupdedup --keep-non-real-cells sample.bam sample_dedup.bam
| 20240130 23:48:34.431 | FATAL | Exception thrown in worker: std::get: wrong index for variant terminate called without an active exception Aborted (core dumped)
The sample.bam was sorted and contained the “CB” “XC” tag, would you please suggest the issue? I also uploaded a short example bam.
sample.bam.gz https://github.com/PacificBiosciences/pbbioconda/files/14105602/sample.bam.gz
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Operating system 5.14.0-162.6.1.el9_1.x86_64 GNU/Linux
Package name isoseq 4.0.0
Conda environment _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bamtools 2.5.2 hdcf5f25_2 bioconda bedtools 2.31.1 hf5e1c6e_0 bioconda bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.23.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge htslib 1.17 h6bc39ce_1 bioconda isoseq 4.0.0 h9ee0642_0 bioconda keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.20.1 hf9c8cef_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libcurl 7.87.0 h6312ad2_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lima 2.9.0 h9ee0642_1 bioconda ncurses 6.4 h59595ed_2 conda-forge openssl 1.1.1w hd590300_0 conda-forge pbccs 6.4.0 h9ee0642_0 bioconda pbmm2 1.13.1 h9ee0642_0 bioconda pbpigeon 1.2.0 h4ac6f70_0 bioconda pbskera 1.2.0 hdfd78af_0 bioconda pbtk 3.1.1 h9ee0642_0 bioconda pip 20.1.1 pyh9f0ad1d_0 conda-forge pyfaidx 0.5.3 py27_0 bioconda pysam 0.8.4 py27_0 bioconda python 2.7.15 h5a48372_1011_cpython conda-forge python_abi 2.7 1_cp27mu conda-forge readline 8.2 h8228510_1 conda-forge samtools 1.18 hd87286a_0 bioconda setuptools 44.0.0 py27_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.44.2 h2c6b66d_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge
Describe the bug Hi, I am trying to process some single cells isoseq data, which the ccs reads were in fastq.gz. I managed to covert the fastq.gz to unaligned bam file. I have followed the the standard single cells isoseq pipeline (https://isoseq.how/umi/examples.html) till the isoseq groupdedup step, which I encounter the following error:
isoseq groupdedup --keep-non-real-cells sample.bam sample_dedup.bam
| 20240130 23:48:34.431 | FATAL | Exception thrown in worker: std::get: wrong index for variant terminate called without an active exception Aborted (core dumped)
The sample.bam was sorted and contained the “CB” “XC” tag, would you please suggest the issue? I also uploaded a short example bam.
sample.bam.gz