sanger-pathogens / snpeffwrapper Goto Github PK

The README says "The GFF must contain the reference sequence in Fasta format"

This seems to explain why our first attempt to use SnpEffWrapper failed (snpEff build could not find the FASTA files in the temporary directory). It would be nice to optionally allow passing a FASTA file for the assembly separately from the GFF file.

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

We have this version of Java installed,

$ java -version
openjdk version "1.8.0_92"
OpenJDK Runtime Environment (Zulu 8.15.0.1-linux64) (build 1.8.0_92-b15)
OpenJDK 64-Bit Server VM (Zulu 8.15.0.1-linux64) (build 25.92-b15, mixed mode)

Hacking the regular expression match = re.match('^java version "1\.7\.[^"]+"$', first_line) to read match = re.match('^openjdk version "1\.8\.[^"]+"$', first_line) in snpEffWrapper/wrapper.py seems to be enough to run the tool.

Is there good reason not to accept openjdk and versions after 1.7.x?