lindenb
commented
4 years ago works for me:
java -jar dist/biostar398854.jar -gtf /path/to/Homo_sapiens.GRCh37.75.gtf -R /path/to/all_chr.fasta /path/to/merged.vcf.gz |
>ENST...
atgcg....check the chromosome names, check the GTF is propertly defined, etc...
Verify
I have followed the exact installation instructions specified at http://lindenb.github.io/jvarkit/Biostar398854.html. My java version is 11 (openjdk 11 2018-09-25, loaded in a guix environment)
Subject of the issue
The jar file does not work (entirely).
Your environment
${JAVA_HOME}/gnu/store/qiimgqwsj7d5pq2d2979kp4bxyfh95zx-profile/bin/java (I am running it in a guix environment)Steps to reproduce
java -jar dist/biostar398854.jar --gtf path/to/gtf --reference path/to/ref/fasta my_vcf_file.vcf > out_CDS.fastawith jdk 11.28 in a guix environment.Expected behaviour
I expect a .fasta file with the alternative coding sequences per sample.
Actual behaviour
When call the .jar file it prints the error message:
There was an error in the input parameters: The following options are required: [-gtf | --gtf], [-R | --reference] [INFO][Launcher]biostar398854 Exited with failure (-1)Which makes sense, as I do not enter any parameters. However, when I do enter parameters, it has no output. The process finishes instantly, which may be an indication something is going wrong, but my files are mostly rather small (only one gtf line, vcf under 1 MB, ref fasta is 2.2 GB though) so it may mean nothing. Either way, I get no output. None of the files are compressed.I do have a few suspicions as to what it could be, but they are wild guesses. Firstly, my reference fasta is not a real fasta with the whole sequence on a single line, but rather like:
I hope that makes sense...
Secondly, it may be because I'm running it in a guix environment. I don't know if there are known issues with that kind of environment? Though, the java in there is working fine. I can print the error message just fine and
java --versionworks well too.