Example output from Rabix executor on CloudNeo CWL:
ubuntu@ip-172-31-20-25:/mnt/data/cloudneo$ ~/rabix-backend-local-1.0.0-rc3/rabix cloudneo.cwl inputs.json
[2017-03-07 18:04:23.529] [INFO] Pulling docker image samtools:cloudneo
[2017-03-07 18:04:23.539] [INFO] Pulling docker image variant-effect-predictor:cloudneo
[2017-03-07 18:04:24.282] [INFO] Running command line: samtools fastq /mnt/data/cloudneo/sample.bam > sample.fastq
[2017-03-07 18:04:24.373] [INFO] Running command line: tar xfz /mnt/data/cloudneo/homo_sapiens_vep_83_GRCh37.tar.gz -C /opt/variant_effect_predictor_83/cache && perl /opt/variant_effect_predictor_83/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl --input_file /mnt/data/cloudneo/sample.vcf --dir /opt/variant_effect_predictor_83/cache --offline --output_file sample.vep.vcf --stats_file sample.vep.vcf_summary.html --filter_common --html --vcf
[2017-03-07 18:04:24.573] [INFO] Job root.samtools_fastq has started
[2017-03-07 18:04:24.831] [INFO] Job root.Variant_Effect_Predictor has started
[2017-03-07 18:05:51.127] [INFO] Job root.samtools_fastq has completed
[2017-03-07 18:05:51.330] [INFO] Pulling docker image bwa:cloudneo
[2017-03-07 18:05:51.358] [INFO] Running command line: bwa aln -e 0 -o 0 /mnt/data/cloudneo/HLA-I_II_CDS.fasta /mnt/data/cloudneo/cloudneo-20170307180422264/root/samtools_fastq/sample.fastq > sample.aln.sai
[2017-03-07 18:05:51.582] [INFO] Job root.bwa_aln has started
[2017-03-07 18:09:39.329] [INFO] Job root.bwa_aln has completed
[2017-03-07 18:09:39.429] [INFO] Pulling docker image bwa:cloudneo
[2017-03-07 18:09:39.467] [INFO] Running command line: bwa samse /mnt/data/cloudneo/HLA-I_II_CDS.fasta /mnt/data/cloudneo/cloudneo-20170307180422264/root/bwa_aln/sample.aln.sai /mnt/data/cloudneo/cloudneo-20170307180422264/root/samtools_fastq/sample.fastq > sample.sam
[2017-03-07 18:09:39.723] [INFO] Job root.bwa_sampe has started
[2017-03-07 18:11:33.157] [INFO] Job root.bwa_sampe has completed
[2017-03-07 18:11:33.228] [INFO] Pulling docker image hlaminer:cloudneo
[2017-03-07 18:11:33.248] [INFO] Running command line: /usr/local/bin/HLAminer_v1.3/bin/HLAminer.pl -a /mnt/data/cloudneo/cloudneo-20170307180422264/root/bwa_sampe/sample.sam -s 500 -h /mnt/data/cloudneo/HLA-I_II_CDS.fasta -e 1
[2017-03-07 18:11:33.482] [INFO] Job root.hlaminer has started
[2017-03-07 18:13:23.139] [INFO] Job root.hlaminer has completed
[2017-03-07 18:15:15.347] [INFO] Job root.Variant_Effect_Predictor has completed
[2017-03-07 18:15:15.429] [INFO] Pulling docker image python:2.7
[2017-03-07 18:15:15.452] [INFO] Running command line: python add_header.py /mnt/data/cloudneo/cloudneo-20170307180422264/root/Variant_Effect_Predictor/sample.vep.vcf > sample.vep.nochr.vcf
[2017-03-07 18:15:15.673] [INFO] Job root.vcf_parser has started
[2017-03-07 18:15:17.166] [INFO] Job root.vcf_parser has completed
[2017-03-07 18:15:17.333] [INFO] Pulling docker image protein-translator:cloudneo
[2017-03-07 18:15:17.364] [INFO] Running command line: Rscript protein_translator.r /mnt/data/cloudneo/Homo_sapiens.GRCh37.75.gtf /mnt/data/cloudneo/HumanProteins.GRCh37.75.csv /mnt/data/cloudneo/cloudneo-20170307180422264/root/vcf_parser/sample.vep.nochr.vcf sample.vep.exome.xls sample.vep.normal.fasta sample.vep.tumor.fasta 10
[2017-03-07 18:15:17.581] [INFO] Job root.Protein_Translator has started
[2017-03-07 18:16:00.082] [INFO] Job root.Protein_Translator has completed
[2017-03-07 18:16:00.230] [INFO] Pulling docker image netmhcpan:cloudneo
[2017-03-07 18:16:00.231] [INFO] Pulling docker image netmhcpan:cloudneo
[2017-03-07 18:16:00.252] [INFO] Running command line: python netmhcpan_parser.py -f /mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.tumor.fasta -hla /mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv -d /mnt/data/cloudneo/netmhcpan-3.0.imgt.fasta -l 9 && mv outputs/* .
[2017-03-07 18:16:00.270] [INFO] Running command line: python netmhcpan_parser.py -f /mnt/data/cloudneo/cloudneo-20170307180422264/root/Protein_Translator/sample.vep.normal.fasta -hla /mnt/data/cloudneo/cloudneo-20170307180422264/root/hlaminer/HLAminer_HPRA.csv -d /mnt/data/cloudneo/netmhcpan-3.0.imgt.fasta -l 9 && mv outputs/* .
[2017-03-07 18:16:00.578] [INFO] Job root.netmhcpan has started
[2017-03-07 18:16:00.727] [INFO] Job root.netmhcpan_1 has started
[2017-03-07 18:23:04.175] [INFO] Job root.netmhcpan has completed
[2017-03-07 18:23:04.185] [INFO] Job root.netmhcpan_1 has completed
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