natechols
commented
4 years ago Handling the new read group ID format requires a newer version of pbcore - I'm not sure what is currently available through pbbioconda, but 2.0 definitely works (although it now requires Python 3).
altayg
Operating system Ubuntu 18.04
Package name isoseq3 3.3.0 (commit v3.3.0) lima 1.11.0 (commit v1.11.0) ccs 4.2.0 (commit v4.2.0)
Conda environment $ conda list
packages in environment at /home/ga/anaconda3/envs/anaCogent5.2:
#
Name Version Build Channel
_anaconda_depends 5.1.0 py27_2
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge alabaster 0.7.12 py_0 conda-forge anaconda custom py27_1
anaconda-client 1.7.2 py_0 conda-forge anaconda-project 0.8.3 py_0 conda-forge argh 0.26.2 py27_1001 conda-forge asn1crypto 1.3.0 py27_0 conda-forge astroid 1.6.5 py27_0 conda-forge astropy 2.0.9 py27_0 conda-forge atomicwrites 1.3.0 py_0 conda-forge attrs 19.3.0 py_0 conda-forge autopep8 1.5 py_0 conda-forge avro-python2 1.9.0 py_0 bioconda babel 2.8.0 py_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge backports.os 0.1.1 py27_1001 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py_1 conda-forge bamtools 2.5.1 he860b03_5 bioconda beautifulsoup4 4.8.2 py27_0 conda-forge biopython 1.76 py27h516909a_0 conda-forge bitarray 1.2.1 py27h516909a_0 conda-forge bkcharts 0.2 py27_0 conda-forge blaze 0.11.3 py27_0 conda-forge bleach 3.1.1 py_0 conda-forge blosc 1.17.1 he1b5a44_0 conda-forge bokeh 1.4.0 py27_0 conda-forge boto 2.49.0 py_0 conda-forge bottleneck 1.3.2 py27hc1659b7_0 conda-forge bx-python 0.8.8 py27h9449cc1_0 bioconda bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2019.11.28 hecc5488_0 conda-forge cairo 1.16.0 hfb77d84_1002 conda-forge cdecimal 2.3 py27h516909a_1001 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge cffi 1.14.0 py27hd463f26_0 conda-forge chardet 3.0.4 py27_1005 conda-forge click 7.0 py_0 conda-forge cloudpickle 1.3.0 py_0 conda-forge clyent 1.2.2 py_1 conda-forge colorama 0.4.3 py_0 conda-forge configparser 3.7.3 py27_1 conda-forge contextlib2 0.6.0.post1 py_0 conda-forge cryptography 2.8 py27h72c5cf5_1 conda-forge curl 7.68.0 hf8cf82a_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.15 py27haf22ab1_1 conda-forge cytoolz 0.10.1 py27h516909a_0 conda-forge dask 1.2.2 py_3 conda-forge dask-core 1.2.2 py_0 conda-forge datashape 0.5.4 py_1 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge diff-match-patch 20181111 py_0 conda-forge distributed 1.28.1 py27_0 conda-forge docutils 0.16 py27h8c360ce_1 conda-forge entrypoints 0.3 py27h8c360ce_1001 conda-forge enum34 1.1.10 py27h8c360ce_1 conda-forge et_xmlfile 1.0.1 py_1001 conda-forge expat 2.2.9 he1b5a44_2 conda-forge fastcache 1.1.0 py27h516909a_0 conda-forge filelock 3.0.10 py_0 conda-forge flake8 3.7.9 py27_0 conda-forge flask 1.1.1 py_1 conda-forge flask-cors 3.0.8 py_0 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.0 he983fc9_1 conda-forge fribidi 1.0.5 h516909a_1002 conda-forge funcsigs 1.0.2 py_3 conda-forge functools32 3.2.3.2 py_3 conda-forge future 0.18.2 py27_0 conda-forge futures 3.3.0 py27_0 conda-forge get_terminal_size 1.0.0 haa9412d_0
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Describe the bug
I am following this pipeline with my own data: https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki/Tutorial:-Installing-and-Running-Iso-Seq-3-using-Conda
I have 6 samples and want to get reference transcriptome from them.
Ath this step "1. Classify full-length reads:", it is suggested that "If you want to analyze all the demultiplexed FL reads together to increase transcript recovery (Example: Same species, different tissues), you must make a combined data set:"
Therefore I run the below command by modifying for my x.fl.bam files to get a single dataset. " dataset create --type ConsensusReadSet combined_demux.consensusreadset.xml \ prefix.5p--barcode1_3p.bam \ prefix.5p--barcode2_3p.bam \ prefix.5p--barcode3_3p.bam ... "
However it did not work and gave the following error? Any solution for this error? as a possible workaround, if I run the 6 .bam files seperately, how can I get the transcriptome out of those 6?
Error message $ dataset create --type ConsensusReadSet combined_demux.consensusreadset.xml demux.NEB_5p--bc1001_3p.bam demux.NEB_5p--bc1002_3p.bam demux.NEB_5p--bc1003_3p.bam demux.NEB_5p--bc1004_3p.bam demux.NEB_5p--bc1005_3p.bam demux.NEB_5p--bc1006_3p.bam invalid literal for int() with base 16: 'e53a6e34/0--1' Traceback (most recent call last): File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcommand/cli/core.py", line 138, in _pacbio_main_runner return_code = exe_main_func(*args, kwargs) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcoretools/dataset.py", line 59, in run return args.func(args) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcoretools/DataSetEntryPoints.py", line 62, in createXml generateIndices=args.generateIndices) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2018, in init super(ReadSet, self).init(*files, *kwargs) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 485, in init self.updateCounts() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2598, in updateCounts self.assertIndexed() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2428, in assertIndexed self._assertIndexed((IndexedBamReader, CmpH5Reader)) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 1975, in _assertIndexed self._openFiles() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2099, in _openFiles resource = IndexedBamReader(location) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 374, in init super(IndexedBamReader, self).init(fname, referenceFastaFname) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 183, in init self._loadReadGroupInfo() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 81, in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/_BamSupport.py", line 58, in rgAsInt return np.int32(int(rgIdString, 16)) ValueError: invalid literal for int() with base 16: 'e53a6e34/0--1' [ERROR] 2020-03-12 23:06:49,633Z [pbcoretools.dataset _pacbio_main_runner 143] invalid literal for int() with base 16: 'e53a6e34/0--1' Traceback (most recent call last): File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcommand/cli/core.py", line 138, in _pacbio_main_runner return_code = exe_main_func(args, kwargs) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcoretools/dataset.py", line 59, in run return args.func(args) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcoretools/DataSetEntryPoints.py", line 62, in createXml generateIndices=args.generateIndices) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2018, in init super(ReadSet, self).init(*files, **kwargs) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 485, in init self.updateCounts() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2598, in updateCounts self.assertIndexed() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2428, in assertIndexed self._assertIndexed((IndexedBamReader, CmpH5Reader)) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 1975, in _assertIndexed self._openFiles() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/dataset/DataSetIO.py", line 2099, in _openFiles resource = IndexedBamReader(location) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 374, in init super(IndexedBamReader, self).init(fname, referenceFastaFname) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 183, in init self._loadReadGroupInfo() File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/BamIO.py", line 81, in _loadReadGroupInfo rgID = rgAsInt(rg["ID"]) File "/home/ga/anaconda3/envs/anaCogent5.2/lib/python2.7/site-packages/pbcore/io/align/_BamSupport.py", line 58, in rgAsInt return np.int32(int(rgIdString, 16)) ValueError: invalid literal for int() with base 16: 'e53a6e34/0--1'
Expected behavior I expected to get this combined datset combined_demux.consensusreadset.xml so that I can run the next command isoseq3 refine --require-polya combined_demux.consensusreadset.xml primers.fasta flnc.bam