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missing libpbcopper #53

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dbtara opened this issue Nov 20, 2018 · 8 comments
Closed

missing libpbcopper #53

dbtara opened this issue Nov 20, 2018 · 8 comments

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@dbtara
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dbtara commented Nov 20, 2018 •
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Operating system
Which operating system and version are you using?
CentOS 6.10

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?
pb-assembly 0.0.2-py27_0 bioconda
Conda environment
What is the result of conda list? (Try to paste that between triple backticks.)

Name Version Build Channel

asn1crypto 0.24.0 py27_1003 conda-forge
avro-python2 1.8.2 py_1 bioconda
bcftools 1.9 h4da6232_0 bioconda
bedtools 2.27.1 he941832_2 bioconda
blas 1.0 mkl
blasr 5.3.2 hac9d22c_3 bioconda
blasr_libcpp 5.3.1 hac9d22c_2 bioconda
bwa 0.7.17 ha92aebf_3 bioconda
bzip2 1.0.6 h470a237_2 conda-forge
ca-certificates 2018.10.15 ha4d7672_0 conda-forge
certifi 2018.10.15 py27_1000 conda-forge
cffi 1.11.5 py27h5e8e0c9_1 conda-forge
chardet 3.0.4 py27_1003 conda-forge
cryptography 2.3.1 py27hdffb7b8_0 conda-forge
cryptography-vectors 2.3.1 py27_1000 conda-forge
curl 7.62.0 h74213dd_0 conda-forge
cython 0.29 py27hfc679d8_0 conda-forge
decorator 4.3.0 py_0 conda-forge
enum34 1.1.6 py27_1001 conda-forge
future 0.17.0 py27_1000 conda-forge
genomicconsensus 2.3.2 py27_3 bioconda
h5py 2.8.0 py27h7eb728f_3 conda-forge
hdf5 1.10.2 hc401514_2 conda-forge
htslib 1.7 0 bioconda
idna 2.7 py27_1002 conda-forge
intel-openmp 2019.0 118
ipaddress 1.0.22 py_1 conda-forge
iso8601 0.1.12 py_1 conda-forge
krb5 1.16.2 hbb41f41_0 conda-forge
libcurl 7.62.0 hbdb9355_0 conda-forge
libdeflate 1.0 h470a237_0 bioconda
libedit 3.1.20170329 haf1bffa_1 conda-forge
libffi 3.2.1 hfc679d8_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.2.0 hdf63c60_3 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libssh2 1.8.0 h5b517e9_2 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge
linecache2 1.0.0 py_1 conda-forge
minimap2 2.14 ha92aebf_0 bioconda
mkl 2019.0 118
mkl_fft 1.0.6 py27_0 conda-forge
mkl_random 1.0.2 py27_0 conda-forge
mummer4 4.0.0beta2 pl526hfc679d8_3 bioconda
ncurses 6.1 hfc679d8_1 conda-forge
networkx 2.2 py_1 conda-forge
nim-falcon 0.0.0 0 bioconda
numpy 1.15.0 py27h1b885b7_0
numpy-base 1.15.0 py27h3dfced4_0
openssl 1.0.2p h470a237_1 conda-forge
pb-assembly 0.0.2 py27_0 bioconda
pb-dazzler 0.0.0 h470a237_0 bioconda
pb-falcon 0.2.4 py27ha92aebf_0 bioconda
pbalign 0.3.1 py27_1 bioconda
pbbam 0.18.0 h1310cd9_1 bioconda
pbcommand 1.1.1 py27_2 bioconda
pbcore 1.6.5 py27_0 bioconda
perl 5.26.2 h470a237_0 conda-forge
pip 18.1 py27_1000 conda-forge
pycparser 2.19 py_0 conda-forge
pyopenssl 18.0.0 py27_1000 conda-forge
pysam 0.14.1 py27hae42fb6_1 bioconda
pysocks 1.6.8 py27_1002 conda-forge
python 2.7.15 h33da82c_4 conda-forge
python-consensuscore 1.1.1 py27h02d93b8_2 bioconda
python-consensuscore2 3.1.0 py27_2 bioconda
python-edlib 1.2.3.post1 py27h470a237_0 bioconda
python-intervaltree 2.1.0 py_0 bioconda
python-msgpack 0.5.6 py27h470a237_0 bioconda
python-sortedcontainers 2.0.5 py_0 bioconda
pytz 2018.7 py_0 conda-forge
readline 7.0 haf1bffa_1 conda-forge
requests 2.20.1 py27_1000 conda-forge
samtools 1.9 h8ee4bcc_1 bioconda
setuptools 40.6.2 py27_0 conda-forge
six 1.11.0 py27_1001 conda-forge
sqlite 3.25.3 hb1c47c0_0 conda-forge
tk 8.6.8 ha92aebf_0 conda-forge
traceback2 1.4.0 py27_0 conda-forge
unittest2 1.1.0 py_0 conda-forge
urllib3 1.23 py27_1001 conda-forge
wheel 0.32.2 py27_0 conda-forge
xz 5.2.4 h470a237_1 conda-forge
zlib 1.2.11 h470a237_3 conda-forge

Describe the bug
A clear and concise description of what the bug is.
I installed pb-assembly using bioconda and was able to run pb-falcon but pb-unzip fails at 4-polish/cns-output step. After investigating further it appears the error actually happened at quiver-run phase where variantCaller failed due to missing libpbcopper.so.4.2, error pasted below.

Error message
Paste the error message / stack.
variantCaller --algorithm=arrow -x 5 -X 120 -q 20 -j 24 -r ../../../quiver-split/refs/000000F/ref.fa aln-000000F.bam -o cns.fasta.gz -o cns.fastq.gz --minConfidence 0 -o cns.vcf
libpbcopper.so.0.4.2: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/pbcommand/cli/core.py", line 138, in _pacbio_main_runner
return_code = exe_main_func(*args, **kwargs)
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/GenomicConsensus-2.3.2-py2.7.egg/GenomicConsensus/main.py", line 340, in args_runner
return tr.main()
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/GenomicConsensus-2.3.2-py2.7.egg/GenomicConsensus/main.py", line 269, in main
self._algorithm = self._algorithmByName(options.algorithm, peekFile)
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/GenomicConsensus-2.3.2-py2.7.egg/GenomicConsensus/main.py", line 57, in _algorithmByName
from GenomicConsensus.arrow import arrow
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/GenomicConsensus-2.3.2-py2.7.egg/GenomicConsensus/arrow/init.py", line 4, in
from . import utils
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/GenomicConsensus-2.3.2-py2.7.egg/GenomicConsensus/arrow/utils.py", line 11, in
import ConsensusCore2 as cc
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/ConsensusCore2.py", line 17, in
_ConsensusCore2 = swig_import_helper()
File "/scicomp/home/bun3/.local/lib/python2.7/site-packages/ConsensusCore2.py", line 16, in swig_import_helper
return importlib.import_module('_ConsensusCore2')
File "/scicomp/groups/OID/NCEZID/DSR/BCFB/usr/bin/miniconda2/denovo_asm/lib/python2.7/importlib/init.py", line 37, in import_module
import(name)
ImportError: libpbcopper.so.0.4.2: cannot open shared object file: No such file or directory

To Reproduce
Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!
This was run on the Exanple Test data greg200k-sv2

Expected behavior
A clear and concise description of what you expected to happen.
I expect the test data to finish running
@pb-dseifert
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Your version of CC2 is massively outdated. Have you tried running conda update --all? Remember to also update your bioconda channel priorities, as these have changed recently.

@dbtara
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dbtara commented Nov 20, 2018

Thanks for the quick response, I was surprised with the version mismatch as well as this was a brand new installation.

After applying your changes i noticed that it downgraded the following packages.

pb-assembly: 0.0.2-py27_0 bioconda --> 0.0.0-py27_8 bioconda
pb-falcon: 0.2.4-py27ha92aebf_0 bioconda --> 0.2.1-py27hf50d5a6_0 bioconda

Now I am wondering if I have set the priorities correct.
channels:

  • defaults
  • bioconda
  • conda-forge
    Any suggestions?

@pb-dseifert
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just try reinstalling pb-assembly and pb-falcon, using explicit version specifiers.

@dbtara
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dbtara commented Nov 20, 2018

ok tried that .. and here is what happens.

if i try to run it as is. I get the same missing library.

if i install pbcopper, the varintCaller seg faults.

@pb-dseifert
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$ ldd miniconda2/lib/python2.7/site-packages/_ConsensusCore2.so
	linux-vdso.so.1 =>  (0x00007ffc6d38d000)
	libpython2.7.so.1.0 => /home/dseifert/miniconda2/lib/python2.7/site-packages/../../libpython2.7.so.1.0 (0x00007f4379b92000)
	libstdc++.so.6 => /home/dseifert/miniconda2/lib/python2.7/site-packages/../../libstdc++.so.6 (0x00007f4379857000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f4379546000)
	libgcc_s.so.1 => /home/dseifert/miniconda2/lib/python2.7/site-packages/../../libgcc_s.so.1 (0x00007f4379334000)
	libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f4379117000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f4378d56000)
	libdl.so.2 => /lib64/libdl.so.2 (0x00007f4378b52000)
	libutil.so.1 => /lib64/libutil.so.1 (0x00007f437894e000)
	/lib64/ld-linux-x86-64.so.2 (0x0000559bc6289000)

CC2 does not link to pbcopper anymore. But here's a red flag: your normal bioconda installation seems to be in /scicomp/groups/OID/NCEZID/DSR/BCFB/usr/bin/miniconda2/, yet you're loading pbcommand from /scicomp/home/bun3/.local/. Have you mucked with user-site dir? See my reply in #6 (comment) for a fix.

@pb-dseifert
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No feedback, I assume this is fixed with the hint I have in the previous comment.

@dbtara
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dbtara commented Nov 23, 2018

Sorry I was out and did not get a chance to test till now. David your diagnosis was correct. Not sure why .local was being picked up. It was not in my current path or settings but was left over from an attempt to install the binaries a while back, using USERBASE method. Thanks this worked

@pb-dseifert
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This is a general python problem: Python will try to load modules in your userbase before loading it from elsewhere. You probably had some stale installation from pip or python setup.py from somewhere.

@NicMAlexandre NicMAlexandre mentioned this issue Mar 13, 2019
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@dbtara @pb-dseifert