Singularity GATK4 permission problem error

[Tintest]

Hello,

I'm trying to use a Singularity container from a Docker image of the GATK4 , a Bioinformatic tool for "Genome" analysis (processing of genetic data).

I got an error which is directly related to Singularity permissions to create a directory ('/root/.theano/compiledir_Linux-4.10--generic-x86_64-with-debian-stretch-sid-x86_64-3.6.2-64'). It's running fine with Singularity when I'm root and Docker (without root). So it's not really a GATK4 problem but more a Singularity-GATK4 related problem.

Do you have any idea make it run properly ? Change my building command ? I need to do not be root when I'm running this tool.

Version of softwares:

Singularity : 2.5.1, GATK : 4.0.4.0

Command

Singularity :
singularity build gatk-4.0.4.0.img docker://broadinstitute/gatk:4.0.4.0

GATK4 :
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/build/libs/gatk-package-4.0.4.0-local.jar DetermineGermlineContigPloidy --input 2044098202-8046_S5_sample.counts.hdf5 --input 2045946179-9076_S2_sample.counts.hdf5 --input 2045946166-9075_S1_sample.counts.hdf5 --input 2048220927-11022_S4_sample.counts.hdf5 --input 2045599261-9046ci_S1_sample.counts.hdf5 --input 2046745668-1007_S5_sample.counts.hdf5 --input 2044098101-8043_S2_sample.counts.hdf5 --input 2044098168-8044_S3_sample.counts.hdf5 --input 2046746598-1012_S4_sample.counts.hdf5 --input 2044395763-8064ci_S4_sample.counts.hdf5 --input 2044395647-8061ci_S1_sample.counts.hdf5 --input 70-20-CI_S3_sample.counts.hdf5 --input 70-18-CI_S1_sample.counts.hdf5 --input 2044395782-8065ci_S5_sample.counts.hdf5 --input 2048222393-11027_S3_sample.counts.hdf5 --input 2048220452-11020_S2_sample.counts.hdf5 --input 2048222667-11031_S7_sample.counts.hdf5 --input 2044395678-8062ci_S2_sample.counts.hdf5 --input 2044395611-8060_S6_sample.counts.hdf5 --input 2048221956-11025_S1_sample.counts.hdf5 --input 2045946131-9071ci_S6_sample.counts.hdf5 --input 2045599349-9047ci_S2_sample.counts.hdf5 --input 2045599158-9045ci_S6_sample.counts.hdf5 --input 2045946149-9073ci_S5_sample.counts.hdf5 --input 2048220431-11019_S1_sample.counts.hdf5 --input 2045946141-9072ci_S4_sample.counts.hdf5 --input 2046746758-1013_S5_sample.counts.hdf5 --input 2045598958-9043ci_S4_sample.counts.hdf5 --input 2046745451-1006_S4_sample.counts.hdf5 --input 2048220997-11023_S5_sample.counts.hdf5 --input 2044097928-8042_S1_sample.counts.hdf5 --input 2045598560-9041ci_S2_sample.counts.hdf5 --input 70-21-CI_S4_sample.counts.hdf5 --input 70-19-CI_S2_sample.counts.hdf5 --input 2046745923-1008_S6_sample.counts.hdf5 --input 2045598771-9042ci_S3_sample.counts.hdf5 --input 2048220861-11021_S3_sample.counts.hdf5 --input 204409765380-40Ci_S6_sample.counts.hdf5 --input 2048221977-11026_S2_sample.counts.hdf5 --input 2048222584-11029_S5_sample.counts.hdf5 --input 2046746353-1010_S2_sample.counts.hdf5 --input 2045946158-9074ci_S6_sample.counts.hdf5 --input 2045946119-9070ci_S5_sample.counts.hdf5 --input 2045599063-9044ci_S5_sample.counts.hdf5 --input 2046746482-1011_S3_sample.counts.hdf5 --input 204409784980-41ci_S7_sample.counts.hdf5 --input 2048222477-11028_S4_sample.counts.hdf5 --input 2045598355-9040ci_S1_sample.counts.hdf5 --input 2048221935-11024_S6_sample.counts.hdf5 --input 2044098183-8045_S4_sample.counts.hdf5 --input 2045946104-9069ci_S4_sample.counts.hdf5 --input 2048222618-11030_S6_sample.counts.hdf5 --input 2046747002-1014_S6_sample.counts.hdf5 --input 2044395737-8063ci_S3_sample.counts.hdf5 --input 2045946189-9077_S3_sample.counts.hdf5 --input 2045599415-9048ci_S3_sample.counts.hdf5 --input 2046746162-1009_S1_sample.counts.hdf5 --contig-ploidy-priors /home/qtestard/PROJECTS/aurexome/REF/common/prior_contig_diploidy.tsv --output /home/qtestard/PROJECTS/aurexome/SAMPLE/CNV_calling/CNV/CNV_calling_NaiveDetermineGermlineContigPloidy --output-prefix CNV_calling_NaiveDetermineGermlineContigPloidy

Actual behavior

PermissionError: [Errno 13] Permission denied: '/root/.theano'

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gcnvkernel/__init__.py", line 1, in <module>
      from pymc3 import __version__ as pymc3_version
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pymc3/__init__.py", line 5, in <module>
      from .distributions import *
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pymc3/distributions/__init__.py", line 1, in <module>
      from . import timeseries
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/pymc3/distributions/timeseries.py", line 1, in <module>
      import theano.tensor as tt
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/__init__.py", line 66, in <module>
      from theano.compile import (
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/compile/__init__.py", line 10, in <module>
      from theano.compile.function_module import *
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/compile/function_module.py", line 21, in <module>
      import theano.compile.mode
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/compile/mode.py", line 10, in <module>
      import theano.gof.vm
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/gof/vm.py", line 662, in <module>
      from . import lazylinker_c
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/gof/lazylinker_c.py", line 42, in <module>
      location = os.path.join(config.compiledir, 'lazylinker_ext')
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/confith.join(config.compiledir, 'lazylinker_ext')
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/configparser.py", line 333, in __get__
      self.__set__(cls, val_str)
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/configparser.py", line 344, in __set__
      self.val = self.filter(val)
    File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/theano/configdefaults.py", line 1745, in filter_compiledir
      " '%s'. Check the permissions." % path)
  ValueError: Unable to create the compiledir directory '/root/.theano/compiledir_Linux-4.10--generic-x86_64-with-debian-stretch-sid-x86_64-3.6.2-64'. Check the permissions.

        at org.broadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
        at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
        at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)
        at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeCommand(PythonScriptExecutor.java:79)
        at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:192)
        at org.broadinstitute.hellbender.tools.copynumber.DetermineGermlineContigPloidy.onStartup(DetermineGermlineContigPloidy.java:240)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:132)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)

Steps to reproduce behavior

Quite difficult to do for you, because I assume your are not familiar with this kind of data / tools. I cannot share you my datasets because they are quite heavy and they are from patient for clinical diagnostic.

If you really need to investigate in real conditions with test files, I could try to find some public available files close to mine.

Thank you.

My thread on GATK4 Github #4782

[jmstover]

Is there some configuration that's looking for the /root/.theano directory? If it's running as your user... I would expect it to be trying to use the directory: /home/qtestard/.theano

[Tintest]

Thank you for your answer.

Honestly I have no idea what's happening in this directory, because before the command and does not exist and after it seems to doesn't exist anymore. I tried to run the container one time in sudo and writable mode with my command hoping it will create all the necessary directories (it worked for severall tools), but when I rerun it, no difference, still the same permission error in the /root directory.

I agree, it would be better to use the /home/qtestard/.theano, but maybe it is a limit of the theano software and so the GATK4 software itself.

[jmstover]

Right. As your user you should not be able to write to the /root directory. If you run the container as root, the host /root is getting mounted writable inside the container. So, if you were to look, there should be a /root/.theano directory on the host.

That's where I'm getting confused. It looks like there's some configuration that has the /root/.theano path hard coded, so when it's ran as a normal user, it's still trying to use that path you don't have access to.

[Tintest]

Indeed it seems quite logical. I will ask the GATK4 devs if looking in the /root directory is a normal behavior and if they could change it.

Thank you :)

[jmstover]

Sounds good. I'm going to close this here. Go a head and re-open it, or start a new issue, if you later run into the same/or similar issue.

-J