errors in mutation lib integration #101
Comments
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Hi,
It looks like it's still having trouble with the DB_File module loading.
Any chance you'd be able to use our Singularity image? It's the easiest /
most robust way of using the software.
https://github.com/NCIP/ctat-mutations/wiki/ctat_mutations_docker_singularity#running-trinity-using-singularity
best,
~brian
…On Mon, Nov 1, 2021 at 1:06 PM aoifgri ***@***.***> wrote:
Hello,
I've been having multiple issues in Step 3 of the installation process
(Execute the mutation lib integration utility). I have directly installed
ctat-mutations and all the libraries and dependencies yet keep encountering
a non-zero exit status. Below is the current issue I am facing, which
hasn't been resolved after installing the DB_File.pm :
python3
ctat-mutations-3.0.0/mutation_lib_prep/ctat-mutation-lib-integration.py
--genome_lib_dir
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/
2021-11-01 16:59:53,947: ref dict created for gatk use in pipe
2021-11-01 16:59:53,948: extracting splice-adjacent regions
Can't locate loadable object for module DB_File in @inc
<https://github.com/inc> ***@***.*** <https://github.com/inc> contains:
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/PerlLib
/usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/PerlLib/TiedHash.pm
line 6.
Compilation failed in require at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/PerlLib/TiedHash.pm
line 6.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/PerlLib/TiedHash.pm
line 6.
Compilation failed in require at (eval 2) line 2.
...propagated at /usr/share/perl5/base.pm line 84.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/PerlLib/Gene_obj_indexer.pm
line 6.
Compilation failed in require at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl line 8.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl line 8.
Traceback (most recent call last):
File
"./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/ctat-mutation-lib-integration.py",
line 82, in
subprocess.check_call(cmd, shell=True)
File "./apps/python3/3.10.0/gcc-4.8.5/lib/python3.10/subprocess.py", line
369, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command
'./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations-3.0.0/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_annot.gtf
>
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat_mutation_lib/ref_annot.splice_adj.bed'
returned non-zero exit status 2.
I am using python3.10 and gatk4.2.2.0, and have installed
ctat-mutations-3.0.0 and have all files in the appropriate locations.
Any help is appreciated. Thanks!
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The Broad Institute
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Hi Brian, I have now tried building the image with singularity pull docker://trinityctat/ctat_mutations and running the singularity code for Step 3 but am getting the following error, with all files in the correct directories:
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hi,
It's not finding the file:
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations.v3.2.0.simg
Try putting the simg file in your current working directory and specifying
it as simply ctat-mutations.v3.2.0.simg
…On Tue, Nov 2, 2021 at 12:56 PM aoifgri ***@***.***> wrote:
Hi Brian,
I have now tried building the image with singularity pull
docker://trinityctat/ctat_mutations and running the singularity code for
Step 3 but am getting the following error, with all files in the correct
directories:
singularity exec -e -B
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations.v3.2.0.simg
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py
--genome_lib_dir
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir
FATAL: could not open image
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations.v3.2.0.simg:
failed to retrieve path for
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations.v3.2.0.simg:
lstat
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations.v3.2.0.simg:
no such file or directory
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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There seemed to be a formatting error which I have now fixed. However I am getting the following when running the same code failing at multiple steps:
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Please keep working with the singularity image. Let's see the command
you're running and the error message that you're experiencing. We'll take
it from there.
If you need to troubleshoot the singularity image, try running it in
interactive mode:
singularity shell -e ctat-mutations.v3.2.0.simg
(type 'exit' to exit the container)
~b
…On Wed, Nov 3, 2021 at 5:51 AM aoifgri ***@***.***> wrote:
There seemed to be a formatting error which I have now fixed. However I am
getting the following when running the same code failing at multiple steps:
2021-11-03 09:45:55,519: ref dict created for gatk use in pipe
2021-11-03 09:45:55,521: extracting splice-adjacent regions
DB_File object version 1.84 does not match bootstrap parameter 1.856 at
/usr/lib/x86_64-linux-gnu/perl/5.28/DynaLoader.pm line 204.
Compilation failed in require at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/PerlLib/TiedHash.pm
line 6.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/PerlLib/TiedHash.pm
line 6.
Compilation failed in require at /usr/share/perl/5.28/base.pm line 135.
...propagated at /usr/share/perl/5.28/base.pm line 157.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/PerlLib/Gene_obj_indexer.pm
line 6.
Compilation failed in require at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl line 8.
BEGIN failed--compilation aborted at
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl line 8.
Traceback (most recent call last):
File
"./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/ctat-mutation-lib-integration.py",
line 82, in
subprocess.check_call(cmd, shell=True)
File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command
'./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat-mutations/mutation_lib_prep/
gencode_gtf_to_splice_adjacent_regions.pl
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_annot.gtf
>
./GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ctat_mutation_lib/ref_annot.splice_adj.bed'
returned non-zero exit status 2.
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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
Hello,
I've been having multiple issues in Step 3 of the installation process (Execute the mutation lib integration utility). I have directly installed ctat-mutations and all the libraries and dependencies yet keep encountering a non-zero exit status. Below is the current issue I am facing, which hasn't been resolved after installing the DB_File.pm :
I am using python3.10 and gatk4.2.2.0, and have installed ctat-mutations-3.0.0 and have all files in the appropriate locations.
Any help is appreciated. Thanks!
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