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manta error in running test data demo #40

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XiongLuoxing opened this issue Jul 9, 2016 · 5 comments
Closed

manta error in running test data demo #40

XiongLuoxing opened this issue Jul 9, 2016 · 5 comments

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@XiongLuoxing
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Dear manta teams:

It is a great pleasure that you have a so well-behaved structural variation calling platform.

I'm trying to use manta. But running demo meets problem. I really want to use your program properly. And sincerely hope that you can give me some advice on how to debug. Really need your help.

The installation seems all right by
manta-0.29.6.release_src.tar.bz2.

My linux version is:
Linux mgt.cluster.com 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux
gcc 4.8.5
python 2.7.12

The installation is the same as:
wget https://github.com/Illumina/manta/releases/download/v${MANTA_VERSION}/manta-${MANTA_VERSION}.release_src.tar.bz2
tar -xjf manta-${MANTA_VERSION}.release_src.tar.bz2
mkdir build && cd build
# Ensure that CC and CXX are updated to target compiler if needed, e.g.:
# export CC=/path/to/cc
# export CXX=/path/to/c++
../manta-${MANTA_VERSION}.release_src/configure --jobs=4 --prefix=/path/to/install
make -j4 install

And while running
runMantaWorkflowDemo.py
in the installation path, the error part of log is like this:

[2016-07-09T21:44:08.978098] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam'
[2016-07-09T21:44:08.991474] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [getAlignmentStats_generateStats_000] Last 6 stderr lines from task (of 6 total lines):
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.904889] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: EXCEPTION: locale::facet::_S_create_c_locale name not valid
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.911776] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] ...caught in program.run()
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.913878] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] cmdline: /Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.915710] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] version: 0.29.6
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.917367] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] buildTime: 2016-07-09T21:25:51.900217Z
[2016-07-09T21:44:08.994892] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] [2016-07-09T21:44:08.919056] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] compiler: g++-4.8.5
[2016-07-09T21:44:08.998084] [mgt.cluster.com] [3563_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
[2016-07-09T21:44:14.596202] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] Worklow terminated due to the following task errors:
[2016-07-09T21:44:14.602155] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'getAlignmentStats_generateStats_000' launched from master workflow, error code: 1, command: '/Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam'
[2016-07-09T21:44:14.606530] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Error Message:
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [getAlignmentStats_generateStats_000] Last 6 stderr lines from task (of 6 total lines):
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.904889] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] FATAL_ERROR: EXCEPTION: locale::facet::_S_create_c_locale name not valid
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.911776] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] ...caught in program.run()
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.913878] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] cmdline: /Share/BP/xionglx/tools/manta-0.29.6-build/libexec/GetAlignmentStats --output-file /Share/BP/xionglx/tools/manta-0.29.6-build/bin/MantaDemoAnalysis/workspace/alignmentStats.xml.tmpdir/alignmentStats.xml.000.xml --align-file /Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.915710] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] version: 0.29.6
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.917367] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] buildTime: 2016-07-09T21:25:51.900217Z
[2016-07-09T21:44:14.610924] [mgt.cluster.com] [3563_1] [WorkflowRunner] [ERROR] [2016-07-09T21:44:08.919056] [mgt.cluster.com] [3563_1] [getAlignmentStats_generateStats_000] compiler: g++-4.8.5

Looking forward to your reply.

Best,
Luoxing.
@ctsa
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ctsa commented Jul 10, 2016

Hi Luoxing,

Sorry for the trouble. Your attached error message includes:

EXCEPTION: locale::facet::_S_create_c_locale name not valid

...suggesting a locale issue. Can you provide the output of the localecommand for your system? This might help us reproduce the issue here.

-Chris

@XiongLuoxing
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Hi Chris,

Thank you very much for the reply.

By locale command output, do you mean this:

[xionglx@mgt ~]$ locale
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_ALL to default locale: No such file or directory
LANG=en_US.iso885915
LC_CTYPE=UTF-8
LC_NUMERIC="en_US.iso885915"
LC_TIME="en_US.iso885915"
LC_COLLATE="en_US.iso885915"
LC_MONETARY="en_US.iso885915"
LC_MESSAGES="en_US.iso885915"
LC_PAPER="en_US.iso885915"
LC_NAME="en_US.iso885915"
LC_ADDRESS="en_US.iso885915"
LC_TELEPHONE="en_US.iso885915"
LC_MEASUREMENT="en_US.iso885915"
LC_IDENTIFICATION="en_US.iso885915"
LC_ALL=

Is there anything wrong about this locale output? How should I recover it?

Best,
Thank you.

@ctsa
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ctsa commented Jul 10, 2016

Thanks, I can reproduce the problem here with:

LC_CTYPE=UTF-8 ./runMantaWorkflowDemo.py

I'm not sure whether the problem is the "UTF-8" value itself, or its lack of consistency with the other LC_* values.

The first part of your locale command response: locale: Cannot set LC_CTYPE to default locale: No such file or directory suggests you may have a configuration issue, but I don't have any experience to make a more specific suggestion here. I will try a few things to see if I can get this working on our side.

@XiongLuoxing
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Thank you very much.

I have reset LC_CTYPE while running ./runMantaWorkflowDemo.py like this:
LC_CTYPE="en_US.UTF8" ./runMantaWorkflowDemo.py

Thus LC_CTYPE is consistent with other LC_* values, and demo could be successfully run with last lines of log like this:

[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner] Manta workflow successfully completed.
[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner]
[2016-07-11T00:32:27.347072] [mgt.cluster.com] [1787_1] [WorkflowRunner] workflow version: 0.29.6
[2016-07-11T00:32:27.349953] [mgt.cluster.com] [1787_1] [WorkflowRunner]
[2016-07-11T00:32:27.352067] [mgt.cluster.com] [1787_1] [WorkflowRunner] Workflow successfully completed all tasks
[2016-07-11T00:32:27.354336] [mgt.cluster.com] [1787_1] [WorkflowRunner] Elapsed time for full workflow: 5 sec

**** Completed demo workflow execution.

**** Starting comparison to expected results.
**** Expected results dir: '/Share/BP/xionglx/tools/manta-0.29.6-build/share/demo/manta/expectedResults'
**** Demo results dir: 'MantaDemoAnalysis/results/variants'

**** No differences between expected and computed results.

**** Demo/verification successfully completed

I will try if resetting LC_CTYPE can make thing work for my own data.

Thank you again!!!

Best,
Luoxing

@ctsa
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ctsa commented Jul 11, 2016

Thanks Luoxing,

I've added a patch to our environment setup which sets LC_ALL to the "C" locale. I've tested that this solves (our reproduction of) the issue you've reported here -- the change will appear in our next Manta version bump.

@ctsa ctsa closed this as completed Jul 11, 2016
x-chen pushed a commit that referenced this issue Aug 17, 2016
@ctsa
[#40] improve robustness to user locale settings
fa077d5 
This forces the "C" locale for the entire pipeline, motivated
by exceptions thrown by boost::filesystem in response to certain
locale configurations.
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@ctsa @XiongLuoxing