Biowulf High Performance Computing at the NIH
jvarkit on Biowulf

Java tools for bioinformatics. Tools are not described in detail here see the author's documentation. Note that all tools are compiled though some of them are pretty lab specific or deprecated.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=6g --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load jvarkit
[user@cn3144]$ cp -L ${JVARKIT_TEST_DATA:-none}/* .
[user@cn3144]$ java -jar $JVARKIT_JARPATH/backlocate.jar --help
Usage: backlocate [options] Files
  Options:
  * -g, --gtf
      A GTF (General Transfer Format) file. See
      https://www.ensembl.org/info/website/upload/gff.html . Please note that
      CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    -p, --printSeq
      print mRNA & protein sequences
      Default: false
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit


[user@cn3144]$ gc=/fdb/GENCODE/Gencode_human/release_35
[user@cn3144]$ gtf=$gc/gencode.v35.primary_assembly.annotation.gtf 
[user@cn3144]$ genome=$gc/GRCh38.primary_assembly.genome.fa

[user@cn3144]$ echo -e "NOTCH2\tPro1090M\tInteresting" \
                    | java -jar $JVARKIT_JARPATH/backlocate.jar \
                        --gtf $gtf -R $genome \
                    | grep -v "##" \
                    | java -jar $JVARKIT_JARPATH/prettytable.jar 
+------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+
| #User.Gene | AA1 | petide.pos.1 | AA2 | transcript.name | transcript.id     | transcript.strand | transcript.AA | index0.in.rna | wild.codon | potential.var.codons | base.in.rna | chromosome | index0.in.genomic | exon                     | messages | extra.user.data |
+------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+
| NOTCH2     | Pro | 1090         | Met | NOTCH2          | ENST00000256646.7 | -                 | P             | 3267          | CCA        | .                    | C           | chr1       | 119937925         | ENST00000256646.7.Exon20 | .        | Interesting     |
| NOTCH2     | Pro | 1090         | Met | NOTCH2          | ENST00000256646.7 | -                 | P             | 3268          | CCA        | .                    | C           | chr1       | 119937924         | ENST00000256646.7.Exon20 | .        | Interesting     |
| NOTCH2     | Pro | 1090         | Met | NOTCH2          | ENST00000256646.7 | -                 | P             | 3269          | CCA        | .                    | A           | chr1       | 119937923         | ENST00000256646.7.Exon20 | .        | Interesting     |
+------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+

[user@cn3144]$ paste <(gunzip -c r1.fastq.gz | paste - - - -) <(gunzip -c r2.fastq.gz | paste - - - -)\
                    | tr "\t" "\n" \
                    | java -jar $JVARKIT_JARPATH/fastqjs.jar \
                        -i -e 'pair.get(0).getReadString().contains("GTTTAAAC") && pair.get(1).getReadString().contains("GTTTAAAC") ' \ 
                    > example.fastq 
[user@cn3144]$ cat <<__EOF__ > filter.js
// prints a VARIATION if two samples at least have a DP<200 
function myfilterFunction()
    {
    var samples=header.genotypeSamples;
    var countOkDp=0;


    for(var i=0; i< samples.size();++i)
        {
        var sampleName=samples.get(i);
        if(! variant.hasGenotype(sampleName)) continue;
        var genotype = variant.genotypes.get(sampleName);
        if( ! genotype.hasDP()) continue;
        var dp= genotype.getDP();
        if(dp < 200 ) countOkDp++;
        }
    return (countOkDp>2)
    }
myfilterFunction();
__EOF__   
[user@cn3144]$ java -jar $JVARKIT_JARPATH/vcffilterjs.jar -f filter.js gatk.vcf
...
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  BLANK   NA12878 NA12891 NA12892 NA19238  NA19239 NA19240
chr22   42526449        .       T       A       151.47  .       AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611   GT:AD:DP:GQ:PL  0/1:23,8:31:99:190,0,694        0/0:188,0:190:99:0,478,5376     0/0:187,0:187:99:0,493,5322      0/0:247,0:249:99:0,634,6728     0/0:185,0:185:99:0,487,5515     0/0:202,0:202:99:0,520,5857      0/0:181,1:182:99:0,440,5362
chr22   42526634        .       T       C       32.60   .       AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276   GT:AD:DP:GQ:PL  0/1:21,4:25:71:71,0,702 0/0:187,2:189:99:0,481,6080     0/0:233,0:233:99:0,667,7351      0/0:230,0:230:99:0,667,7394     0/0:174,1:175:99:0,446,5469     0/0:194,2:196:99:0,498,6239      0/0:174,0:175:99:0,511,5894
chr22   42527793        rs1080989       C       T       3454.66 .       AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618       GT:AD:DP:GQ:PL  ./.     0/1:72,90:162:99:1699,0,1767    0/1:103,96:202:99:1756,0,2532    0/0:188,0:188:99:0,526,5889     0/0:160,0:160:99:0,457,4983     0/0:197,0:198:99:0,544,6100      0/0:156,0:156:99:0,439,5041

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. jvarkit.sh), which uses the input file 'jvarkit.in'. For example:

#!/bin/bash
module load jvarkit/20200713
paste <(gunzip -c r1.fastq.gz | paste - - - -) <(gunzip -c r2.fastq.gz | paste - - - -) \
    | tr "\t" "\n" \
    | java -jar $JVARKIT_JARPATH/fastqjs.jar \
        -i -e 'pair.get(0).getReadString().contains("GTTTAAAC") && pair.get(1).getReadString().contains("GTTTAAAC") ' \ 
    > example.fastq

Submit this job using the Slurm sbatch command.

sbatch --mem=2g jvarkit.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. jvarkit.swarm). For example:

echo -e "NOTCH2\tP1090M\tInteresting" | java -jar $JVARKIT_JARPATH/backlocate.jar --gtf hg19.gtf -R hg19.fa > notch_P1090M
echo -e "NOTCH2\tP1090I\tInteresting" | java -jar $JVARKIT_JARPATH/backlocate.jar --gtf hg19.gtf -R hg19.fa > notch_P1090I

Submit this job using the swarm command.

swarm -f jvarkit.swarm -g 2 --module jvarkit/20200713
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module jvarkit Loads the jvarkit module for each subjob in the swarm