I've pasted below the command and error message I get from SnpEffWrapper. I have checked (via another user) that I have merged my GFF and fasta file correctly so that doesn't seem to be the issue. I am happy to upload the gff and fasta file if it isn't clear from the error message what the issue is. I will add that my vcf was generated by freebayes with 4 samples, in case that might affect things.
[2018-10-22 12:25:51,163] INFO: Checking that the VCF and GFF contigs are consistent
[2018-10-22 12:25:52,312] INFO: Building snpeff database
Traceback (most recent call last):
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 222, in _snpeff_build_database
subprocess.check_call(command, stdout=stdout, stderr=stderr)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/bin/java', '-Xmx4g', '-jar', '/media/sf_SharedDrive/Download/snpEff/snpEff.jar', 'build', '-gff3', '-verbose', 'data', '-c', '/home/manager/WGS/WGS analysis/snpeff_data_dir_b6d9iqrh/config']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/manager/miniconda3/envs/ddocent_env/bin/snpEffBuildAndRun", line 45, in
annotate_vcf(args)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 343, in annotate_vcf
args.vcf_file, config_filename, args.debug)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 275, in run_snpeff
build_stderr)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 224, in _snpeff_build_database
raise BuildDatabaseError("Problem building the database from your GFF")
snpEffWrapper.wrapper.BuildDatabaseError: Problem building the database from your GFF
Hey!
I've pasted below the command and error message I get from SnpEffWrapper. I have checked (via another user) that I have merged my GFF and fasta file correctly so that doesn't seem to be the issue. I am happy to upload the gff and fasta file if it isn't clear from the error message what the issue is. I will add that my vcf was generated by freebayes with 4 samples, in case that might affect things.
Thanks!
Gordon
snpEffBuildAndRun --snpeff-exec /media/sf_SharedDrive/Download/snpEff/snpEff.jar --java-exec /usr/bin/java --coding-table 'default: Standard' ./GFF/TriTrypDB-39_TbruceiLister427_Genome_fasta.gff ./freebayes/Allbam.vcf -o ./snpEFF/Allbam.annotated.vcf
[2018-10-22 12:25:51,163] INFO: Checking that the VCF and GFF contigs are consistent [2018-10-22 12:25:52,312] INFO: Building snpeff database Traceback (most recent call last): File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 222, in _snpeff_build_database subprocess.check_call(command, stdout=stdout, stderr=stderr) File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/java', '-Xmx4g', '-jar', '/media/sf_SharedDrive/Download/snpEff/snpEff.jar', 'build', '-gff3', '-verbose', 'data', '-c', '/home/manager/WGS/WGS analysis/snpeff_data_dir_b6d9iqrh/config']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/manager/miniconda3/envs/ddocent_env/bin/snpEffBuildAndRun", line 45, in
annotate_vcf(args)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 343, in annotate_vcf
args.vcf_file, config_filename, args.debug)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 275, in run_snpeff
build_stderr)
File "/home/manager/miniconda3/envs/ddocent_env/lib/python3.6/site-packages/snpEffWrapper/wrapper.py", line 224, in _snpeff_build_database
raise BuildDatabaseError("Problem building the database from your GFF")
snpEffWrapper.wrapper.BuildDatabaseError: Problem building the database from your GFF