brianjohnhaas
commented
2 years ago 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.
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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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
aoifgri
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!