-<pre><code>
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get 2463fa9efeb75e099685528b3b9071e0+438/ .</span>
-156 MiB / 156 MiB 100.0%
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get ae480c5099b81e17267b7445e35b4bc7+180/ .</span>
-23 MiB / 23 MiB 100.0%
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">cwltool bwa-mem-input.yml bwa-mem-input-local.yml</span>
-cwltool 1.0.20160629140624
-[job bwa-mem.cwl] /home/peter/.arvbox/arvbox/arvados/doc/user/cwl/bwa-mem$ docker \
- run \
- -i \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.ann:/var/lib/cwl/job979368791_bwa-mem/19.fasta.ann:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.sa:/var/lib/cwl/job979368791_bwa-mem/19.fasta.sa:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.amb:/var/lib/cwl/job979368791_bwa-mem/19.fasta.amb:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.pac:/var/lib/cwl/job979368791_bwa-mem/19.fasta.pac:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.bwt:/var/lib/cwl/job979368791_bwa-mem/19.fasta.bwt:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem:/var/spool/cwl:rw \
- --volume=/tmp/tmpgzyou9:/tmp:rw \
- --workdir=/var/spool/cwl \
- --read-only=true \
- --log-driver=none \
- --user=1001 \
- --rm \
- --env=TMPDIR=/tmp \
- --env=HOME=/var/spool/cwl \
- biodckr/bwa \
- bwa \
- mem \
- -t \
- 1 \
- -R \
- '@RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129' \
- /var/lib/cwl/job979368791_bwa-mem/19.fasta \
- /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq \
- /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq > /home/peter/.arvbox/arvbox/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam
-[M::bwa_idx_load_from_disk] read 0 ALT contigs
-[M::process] read 100000 sequences (10000000 bp)...
-[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 4745, 1, 0)
-[M::mem_pestat] skip orientation FF as there are not enough pairs
-[M::mem_pestat] analyzing insert size distribution for orientation FR...
-[M::mem_pestat] (25, 50, 75) percentile: (154, 181, 214)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 334)
-[M::mem_pestat] mean and std.dev: (185.63, 44.88)
-[M::mem_pestat] low and high boundaries for proper pairs: (1, 394)
-[M::mem_pestat] skip orientation RF as there are not enough pairs
-[M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 100000 reads in 9.848 CPU sec, 9.864 real sec
-[main] Version: 0.7.12-r1039
-[main] CMD: bwa mem -t 1 -R @RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129 /var/lib/cwl/job979368791_bwa-mem/19.fasta /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq
-[main] Real time: 10.061 sec; CPU: 10.032 sec
-Final process status is success
-{
- "aligned_sam": {
- "size": 30738959,
- "path": "/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam",
- "checksum": "sha1$0c668cca45fef02397bb5302880526d300ee4dac",
- "class": "File"
- }
-}