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rabix / bunny

[Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0
http://rabix.io
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SBG_Prepare_Intervals Failed evaluating expression interval bed error #411

Closed gezthxbio closed 6 years ago

gezthxbio commented 6 years ago

wholegs.cwl.txt Trying to execute Whole Genome Sequencing - BWA + GATK 4.0 (with Metrics) cwl on a small data with interval bed chr12.bed.txt file containing information for 2 chromosomes. rabix command

/home/biouser/bin/rabix-cli-1.0.4/rabix wholegs.cwl -- --fastq small_data/10049_R1.fastq  --fastq small_data/10049_R2.fastq \
        --dbsnp /home/biouser/AGBL_LABS/GATK_FILES/dbsnp_138.hg19.vcf \
        --hapmap /home/biouser/AGBL_LABS/GATK_FILES/hapmap_3.3.hg19.sites.vcf \
        --known_indels_1000g_bqsr /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.indels.hg19.sites.vcf \
        --mills /home/biouser/AGBL_LABS/GATK_FILES/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
        --omni_1000g /home/biouser/AGBL_LABS/GATK_FILES/1000G_omni2.5.hg19.sites.vcf \
        --phase1_snp_1000g /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
        --reference chr12.fasta \
        --intervals_file chr12.bed \
        --memory_per_job 5120MB \
        --threads 15

Got the following error

[2018-01-22 13:42:04.518] [ERROR] Failed to execute status command for root.SBG_Prepare_Intervals. Could not collect outputs.
org.rabix.executor.ExecutorException: Could not collect outputs.
        at org.rabix.executor.handler.impl.JobHandlerImpl.postprocess(JobHandlerImpl.java:318) ~[rabix-cli.jar:na]
        at org.rabix.executor.execution.command.StatusCommand.run(StatusCommand.java:52) ~[rabix-cli.jar:na]
        at org.rabix.executor.execution.JobHandlerCommand.run(JobHandlerCommand.java:51) [rabix-cli.jar:na]
        at org.rabix.executor.execution.JobHandlerRunnable.run(JobHandlerRunnable.java:58) [rabix-cli.jar:na]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_162]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_162]
        at java.lang.Thread.run(Thread.java:748) [na:1.8.0_162]
Caused by: org.rabix.bindings.BindingException: org.rabix.bindings.sb.expression.SBExpressionException: Failed to evaluate outputEval.
        at org.rabix.bindings.sb.SBProcessor.postprocess(SBProcessor.java:144) ~[rabix-cli.jar:na]
        at org.rabix.bindings.sb.SBBindings.postprocess(SBBindings.java:79) ~[rabix-cli.jar:na]
        at org.rabix.executor.handler.impl.JobHandlerImpl.postprocess(JobHandlerImpl.java:278) ~[rabix-cli.jar:na]
        ... 6 common frames omitted
Caused by: org.rabix.bindings.sb.expression.SBExpressionException: Failed to evaluate outputEval.
        at org.rabix.bindings.sb.helper.SBBindingHelper.evaluateOutputEval(SBBindingHelper.java:111) ~[rabix-cli.jar:na]
        at org.rabix.bindings.sb.SBProcessor.collectOutput(SBProcessor.java:266) ~[rabix-cli.jar:na]
        at org.rabix.bindings.sb.SBProcessor.collectOutput(SBProcessor.java:235) ~[rabix-cli.jar:na]
        at org.rabix.bindings.sb.SBProcessor.collectOutputs(SBProcessor.java:162) ~[rabix-cli.jar:na]
        at org.rabix.bindings.sb.SBProcessor.postprocess(SBProcessor.java:129) ~[rabix-cli.jar:na]
        ... 8 common frames omitted`
Caused by: org.rabix.bindings.sb.expression.SBExpressionException: Failed evaluating expression { rows = $self[0].contents
  if (rows[rows.length -1] == '\n'){
    rows = rows.split(/\r?\n/).slice(0,-1);
  }
  else {
    rows = rows.split(/\r?\n/);
  }
  out_list = []
  for (i=0; i<rows.length; i++)
  {
    row = rows[i];
    chromosome = row.split("\t")[0];
    start = row.split("\t")[1];
    end = row.split("\t")[2];
    if(typeof start !== "undefined"){
        interval = chromosome.concat(":", start, "-", end);
    }
    else{
        interval = chromosome
    }
    out_list.push(interval);
  }
  return out_list;

}

Full nohup nohup.out.txt

Rabix 1.0.4 CentOS 7 64bit server Docker version 18.01.0-ce, build 03596f5

milos-ljubinkovic commented 6 years ago

Is your docker server running? The nohup.out.txt log shows a lot of docker connection errors on the first glance.

You can check by running "docker ps" or a similar docker cli command.

gezthxbio commented 6 years ago

docker ps -a output

CONTAINER ID        IMAGE                                                          COMMAND                  CREATED             STATUS                   PORTS               NAMES
3e4ce99dd4a2        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       confident_chatterjee
eb4c0096ea61        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       festive_visvesvaraya
2e84570c70f3        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       goofy_leavitt
9e520b64da5b        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       cranky_poitras
04c254904528        images.sbgenomics.com/vladimirk/bwa:0.7.13                     "/bin/sh -c '/opt/bw…"   4 hours ago         Exited (0) 4 hours ago                       brave_kowalevski
e8f39abcac64        images.sbgenomics.com/markop/sbg-decompressor:1.0              "/bin/sh -c 'echo Pa…"   4 hours ago         Exited (0) 4 hours ago                       boring_dubinsky
ee1b7476eb64        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       confident_fermi
63b3456e0962        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       blissful_nobel
247a939f9869        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       focused_leavitt
f437e799eb40        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       suspicious_engelbart
480a4f2d6ef6        images.sbgenomics.com/vladimirk/bwa:0.7.13                     "/bin/sh -c '/opt/bw…"   4 hours ago         Exited (0) 4 hours ago                       pedantic_liskov
c1077e1ad49f        images.sbgenomics.com/markop/sbg-decompressor:1.0              "/bin/sh -c 'echo Pa…"   4 hours ago         Exited (0) 4 hours ago                       romantic_liskov
eefee9f88e3c        images.sbgenomics.com/vladimirk/bwa:0.7.13                     "/bin/sh -c '/opt/bw…"   4 hours ago         Exited (2) 4 hours ago                       thirsty_noether
f1f5fcd40909        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       unruffled_hermann
ed72575ae30b        images.sbgenomics.com/mladenlsbg/fastqc:0.11.4                 "/bin/sh -c 'fastqc …"   4 hours ago         Exited (0) 4 hours ago                       boring_murdock
f738a7fb340b        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       awesome_euler
1950143c982a        images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:1.0   "/bin/sh -c 'python …"   4 hours ago         Exited (2) 4 hours ago                       upbeat_lewin
eadfe868fa28        images.sbgenomics.com/markop/sbg-decompressor:1.0              "/bin/sh -c 'echo Pa…"   4 hours ago         Exited (0) 4 hours ago                       amazing_bhaskara
0de7851bd122        abdolab/tychus-assembly                                        "echo"                   4 days ago          Exited (0) 4 days ago                        peaceful_bardeen
f888f2fe5b56        abdolab/tychus-assembly                                        "ls /bin"                4 days ago          Exited (0) 4 days ago                        stoic_hamilton
milos-ljubinkovic commented 6 years ago

Seems like it pulled some images and started some containers but at a certain point docker server started throwing out 404 errors. What machine are you running this on and have you tried to restart the docker server/deamon and start this task again? Maybe with images already pulled and extracted it will behave better.

gezthxbio commented 6 years ago

Server : Dell PowerEdge T620 Machine : CentOS Linux release 7.4.1708 (Core) Kernel : Linux 3.10.0-514.16.1.el7.x86_64 x86_64

restarted docker service

systemctl status docker -l output

● docker.service - Docker Application Container Engine
   Loaded: loaded (/usr/lib/systemd/system/docker.service; enabled; vendor preset: disabled)
   Active: active (running) since Tue 2018-01-23 09:08:52 +04; 48s ago
     Docs: https://docs.docker.com
 Main PID: 25029 (dockerd)
   Memory: 42.9M
   CGroup: /system.slice/docker.service
           ├─25029 /usr/bin/dockerd
           └─25044 docker-containerd --config /var/run/docker/containerd/containerd.toml

Jan 23 09:08:51 qmaster.local dockerd[25029]: time="2018-01-23T09:08:51.133670040+04:00" level=info msg="[graphdriver] using prior storage driver: overlay2"
Jan 23 09:08:51 qmaster.local dockerd[25029]: time="2018-01-23T09:08:51.338245511+04:00" level=info msg="Graph migration to content-addressability took 0.00 seconds"
Jan 23 09:08:51 qmaster.local dockerd[25029]: time="2018-01-23T09:08:51.340545134+04:00" level=info msg="Loading containers: start."
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.609407030+04:00" level=info msg="Default bridge (docker0) is assigned with an IP address 172.17.0.0/16. Daemon option --bip can be used to set a preferred IP address"
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.762391527+04:00" level=info msg="Loading containers: done."
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.777372295+04:00" level=warning msg="Not using native diff for overlay2, this may cause degraded performance for building images: opaque flag erroneously copied up, consider update to kernel 4.8 or later to fix"
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.793611707+04:00" level=info msg="Docker daemon" commit=03596f5 graphdriver(s)=overlay2 version=18.01.0-ce
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.793759839+04:00" level=info msg="Daemon has completed initialization"
Jan 23 09:08:52 qmaster.local dockerd[25029]: time="2018-01-23T09:08:52.802457640+04:00" level=info msg="API listen on /var/run/docker.sock"
Jan 23 09:08:52 qmaster.local systemd[1]: Started Docker Application Container Engine.

Did a manual docker pull of all images mentioned in cwl and tried to execute the cwl file. Got this Errror nohup.out2.txt

gezthxbio commented 6 years ago

docker version

Client:
 Version:       18.01.0-ce
 API version:   1.35
 Go version:    go1.9.2
 Git commit:    03596f5
 Built: Wed Jan 10 20:07:19 2018
 OS/Arch:       linux/amd64
 Experimental:  false
 Orchestrator:  swarm

Server:
 Engine:
  Version:      18.01.0-ce
  API version:  1.35 (minimum version 1.12)
  Go version:   go1.9.2
  Git commit:   03596f5
  Built:        Wed Jan 10 20:10:58 2018
  OS/Arch:      linux/amd64
  Experimental: false

docker info

Containers: 85
 Running: 0
 Paused: 0
 Stopped: 85
Images: 12
Server Version: 18.01.0-ce
Storage Driver: overlay2
 Backing Filesystem: xfs
 Supports d_type: true
 Native Overlay Diff: false
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge host macvlan null overlay
 Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 89623f28b87a6004d4b785663257362d1658a729
runc version: b2567b37d7b75eb4cf325b77297b140ea686ce8f
init version: 949e6fa
Security Options:
 seccomp
  Profile: default
Kernel Version: 3.10.0-514.16.1.el7.x86_64
Operating System: CentOS Linux 7 (Core)
OSType: linux
Architecture: x86_64
CPUs: 32
Total Memory: 283.2GiB
Name: qmaster.local
ID: RAMK:S25G:6JMA:J4HW:CLRB:47SD:LJ7E:SR2A:DYZG:EEBY:IHSV:AKJY
Docker Root Dir: /home/biouser/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
 127.0.0.0/8
Live Restore Enabled: false
milos-ljubinkovic commented 6 years ago

Ok, the error is the outputEval expression on the prepare_intervals step

python sbg_prepare_intervals.py --bed /home/biouser/AGBL_LABS/rabix/WGS_TEST/wholegs-2018-01-23-161748.922/root/SBG_Prepare_Intervals/chr12.bed --mode 4

Command either creates no files or the glob expression is resolved badly or the contents of a file aren't loaded properly.

Have you tried to run the latest revision of the Whole Genome workflow? It seems that the sbg public app is up to revision 56 and the tool in question has simpler expressions now so that might change the behaviour or give us a better image of what is happening.

gezthxbio commented 6 years ago

Ok, will try that and post the result.

gezthxbio commented 6 years ago

wgs58.cwl.json.txt Docker pull by rabix failed again, so did a manual pull of all images. executed 

/home/biouser/bin/rabix-cli-1.0.4/rabix wgs58.cwl.json -- --fastq small_data/10049_R1.fastq --fastq small_data/10049_R2.fastq \
        --1000g_indels /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.indels.hg19.sites.vcf \
        --1000g_omni /home/biouser/AGBL_LABS/GATK_FILES/1000G_omni2.5.hg19.sites.vcf \
        --1000g_p1_snps /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
        --bed_file_1 chr12.bed \
        --bqsr_intervals 2 \
        --database_1 /home/biouser/bin/snpEff_latest_core/database/snpEff_v4_3_GRCh37.75.zip \
        --dbsnp /home/biouser/AGBL_LABS/GATK_FILES/dbsnp_138.hg19.vcf \
        --hapmap /home/biouser/AGBL_LABS/GATK_FILES/hapmap_3.3.hg19.sites.vcf \
        --mills /home/biouser/AGBL_LABS/GATK_FILES/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
        --reference chr12.fasta

output

[2018-01-23 22:31:05.607] [INFO] Job root.SBG_Prepare_VQSR_Mills has started
[2018-01-23 22:31:05.607] [INFO] Job root.SBG_Prepare_VQSR_Omni has started
[2018-01-23 22:31:05.607] [INFO] Job root.SBG_Prepare_VQSR_HapMap has started
[2018-01-23 22:31:05.607] [INFO] Job root.SBG_Prepare_VQSR_dbSNP has started
[2018-01-23 22:31:05.607] [INFO] Job root.SBG_Prepare_VQSR_1000G has started
[2018-01-23 22:31:05.610] [INFO] Job root.BWA_INDEX has started
[2018-01-23 22:31:05.610] [INFO] Job root.FastQC has started
[2018-01-23 22:31:05.610] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has started
[2018-01-23 22:31:05.610] [INFO] Job root.SBG_Untar_fasta has started
[2018-01-23 22:31:05.610] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has started
[2018-01-23 22:31:06.173] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 22:31:06.179] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 22:31:06.846] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 22:31:06.958] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 22:31:06.958] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 22:31:07.090] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 22:31:07.134] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 22:31:07.134] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 22:31:07.354] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 22:31:08.593] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/bwa:0.7.13
[2018-01-23 22:31:08.593] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 22:31:08.659] [INFO] Running command line: /opt/bwa-0.7.13/bwa index chr12.fasta ' '' '' '' '' ' ; tar -cf chr12.fasta.tar chr12.fasta *.amb *.ann *.bwt *.pac *.sa
[2018-01-23 22:31:08.668] [INFO] Pulling docker image images.sbgenomics.com/markop/sbg-decompressor:1.0
[2018-01-23 22:31:08.668] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 22:31:08.878] [INFO] Running command line: echo Passing input file 
[2018-01-23 22:31:09.212] [INFO] Job root.SBG_Prepare_VQSR_Mills has completed
[2018-01-23 22:31:10.736] [INFO] Job root.SBG_Prepare_VQSR_Omni has completed
[2018-01-23 22:31:11.249] [INFO] Job root.SBG_Prepare_VQSR_HapMap has completed
[2018-01-23 22:31:13.974] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-23 22:31:13.975] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 22:31:14.002] [INFO] Running command line: python3 sbg_fastq_quality_scale_adjuster.py' '--fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-23-223103.45/root/SBG_FASTQ_Quality_Adjuster/2/10049_R2.fastq
[2018-01-23 22:31:14.041] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-23 22:31:14.041] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 22:31:14.227] [INFO] Running command line: python3 sbg_fastq_quality_scale_adjuster.py' '--fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-23-223103.45/root/SBG_FASTQ_Quality_Adjuster/1/10049_R1.fastq
[2018-01-23 22:31:15.238] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 failed with exit code 2. with message: python3: can't open file 'sbg_fastq_quality_scale_adjuster.py --fastq': [Errno 2] No such file or directory

Job root.SBG_FASTQ_Quality_Adjuster.2 failed with exit code 2. with message: python3: can't open file 'sbg_fastq_quality_scale_adjuster.py --fastq': [Errno 2] No such file or directory
milos-ljubinkovic commented 6 years ago

The docker issues seem to be constant on CentOS from what we've heard from other users as well. We'll see about what can be done but it seems to be on the docker daemon side.

Also that command line issue you just happened upon was introduced in 1.0.4 and I've just made a new release with a fix for it, sorry about that. You can find it here: https://github.com/rabix/bunny/releases/download/v1.0.4-2/rabix-cli-1.0.4.tar.gz

gezthxbio commented 6 years ago

Tried running using the latest release.

[2018-01-23 23:37:51.161] [INFO] Job root.SBG_Untar_fasta has started
[2018-01-23 23:37:51.162] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has started
[2018-01-23 23:37:51.161] [INFO] Job root.SBG_Prepare_VQSR_dbSNP has started
[2018-01-23 23:37:51.161] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has started
[2018-01-23 23:37:51.161] [INFO] Job root.SBG_Prepare_VQSR_Omni has started
[2018-01-23 23:37:51.163] [INFO] Job root.SBG_Prepare_VQSR_Mills has started
[2018-01-23 23:37:51.163] [INFO] Job root.BWA_INDEX has started
[2018-01-23 23:37:51.163] [INFO] Job root.FastQC has started
[2018-01-23 23:37:51.163] [INFO] Job root.SBG_Prepare_VQSR_1000G has started
[2018-01-23 23:37:51.163] [INFO] Job root.SBG_Prepare_VQSR_HapMap has started
[2018-01-23 23:37:51.749] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 23:37:51.755] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 23:37:52.411] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 23:37:52.520] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 23:37:52.520] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 23:37:52.660] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 23:37:52.676] [INFO] Pulling docker image ubuntu:14.04
[2018-01-23 23:37:52.676] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-23 23:37:52.920] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-23 23:37:54.203] [INFO] Pulling docker image images.sbgenomics.com/markop/sbg-decompressor:1.0
[2018-01-23 23:37:54.203] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 23:37:54.238] [INFO] Running command line: echo Passing input file
[2018-01-23 23:37:54.261] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/bwa:0.7.13
[2018-01-23 23:37:54.262] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 23:37:54.471] [INFO] Running command line: /opt/bwa-0.7.13/bwa index chr12.fasta       ; tar -cf chr12.fasta.tar chr12.fasta *.amb *.ann *.bwt *.pac *.sa
[2018-01-23 23:37:54.731] [INFO] Job root.SBG_Prepare_VQSR_Mills has completed
[2018-01-23 23:37:56.276] [INFO] Job root.SBG_Prepare_VQSR_Omni has completed
[2018-01-23 23:37:56.811] [INFO] Job root.SBG_Prepare_VQSR_HapMap has completed
[2018-01-23 23:37:59.535] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-23 23:37:59.535] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 23:37:59.563] [INFO] Running command line: python3 sbg_fastq_quality_scale_adjuster.py --fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-23-233748.748/root/SBG_FASTQ_Quality_Adjuster/2/10049_R2.fastq --no_conversion
[2018-01-23 23:37:59.629] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-23 23:37:59.629] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-23 23:37:59.759] [INFO] Running command line: python3 sbg_fastq_quality_scale_adjuster.py --fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-23-233748.748/root/SBG_FASTQ_Quality_Adjuster/1/10049_R1.fastq --no_conversion
[2018-01-23 23:38:00.773] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 failed with exit code 1. with message: Traceback (most recent call last):
  File "sbg_fastq_quality_scale_adjuster.py", line 117, in <module>
    input_metadata = cwl.inputs['fastq']['metadata']
KeyError: 'metadata'

Job root.SBG_FASTQ_Quality_Adjuster.2 failed with exit code 1. with message: Traceback (most recent call last):
  File "sbg_fastq_quality_scale_adjuster.py", line 117, in <module>
    input_metadata = cwl.inputs['fastq']['metadata']
KeyError: 'metadata'
milos-ljubinkovic commented 6 years ago

It looks like the sbg tool requires the inputs to have sbg metadata. So you would have to create an input file where all the inputs are defined with their appropriate metadata instead of just defining them in the command line as you did in your first post.

It would look something like:

{
"fastq":[
  {
    "path":"small_data/10049_R1.fastq",
    "class":"File",
    "sbg:metadata":{}
  },
  {
    "path":"small_data/10049_R2.fastq",
    "class":"File",
    "sbg:metadata":{}
  }
],

....

Not really sure if any metadata fields are required or is it enough to have them empty but you can see the existing metadata from the files on the sbg platform.

gezthxbio commented 6 years ago

Fixed the meta data by providing --used_quality_scale illumina18 but sbg prepare intervals eval expression failed 

[2018-01-25 13:59:10.712] [INFO] Job root.SBG_Prepare_VQSR_1000G has started
[2018-01-25 13:59:10.711] [INFO] Job root.BWA_INDEX has started
[2018-01-25 13:59:10.711] [INFO] Job root.SBG_Untar_fasta has started
[2018-01-25 13:59:10.711] [INFO] Job root.SBG_Prepare_VQSR_Mills has started
[2018-01-25 13:59:10.711] [INFO] Job root.SBG_Prepare_VQSR_HapMap has started
[2018-01-25 13:59:10.711] [INFO] Job root.SBG_Prepare_VQSR_Omni has started
[2018-01-25 13:59:10.713] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has started
[2018-01-25 13:59:10.713] [INFO] Job root.FastQC has started
[2018-01-25 13:59:10.713] [INFO] Job root.SBG_Prepare_VQSR_dbSNP has started
[2018-01-25 13:59:10.713] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has started
[2018-01-25 13:59:11.278] [INFO] Pulling docker image ubuntu:14.04
[2018-01-25 13:59:11.284] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-25 13:59:11.948] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-25 13:59:12.101] [INFO] Pulling docker image ubuntu:14.04
[2018-01-25 13:59:12.102] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-25 13:59:12.227] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-25 13:59:12.280] [INFO] Pulling docker image ubuntu:14.04
[2018-01-25 13:59:12.281] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-25 13:59:12.516] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-25 13:59:13.738] [INFO] Pulling docker image images.sbgenomics.com/markop/sbg-decompressor:1.0
[2018-01-25 13:59:13.738] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:13.777] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/bwa:0.7.13
[2018-01-25 13:59:13.778] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:13.781] [INFO] Running command line: echo Passing input file
[2018-01-25 13:59:14.008] [INFO] Running command line: /opt/bwa-0.7.13/bwa index chr12.fasta       ; tar -cf chr12.fasta.tar chr12.fasta *.amb *.ann *.bwt *.pac *.sa
[2018-01-25 13:59:14.300] [INFO] Job root.SBG_Prepare_VQSR_Mills has completed
[2018-01-25 13:59:15.844] [INFO] Job root.SBG_Prepare_VQSR_Omni has completed
[2018-01-25 13:59:16.398] [INFO] Job root.SBG_Prepare_VQSR_HapMap has completed
[2018-01-25 13:59:19.258] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-25 13:59:19.258] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:19.286] [INFO] Running command line: echo No conversion
[2018-01-25 13:59:19.360] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-25 13:59:19.360] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:19.491] [INFO] Running command line: echo No conversion
[2018-01-25 13:59:20.349] [INFO] Job root.SBG_Untar_fasta has completed
[2018-01-25 13:59:20.402] [INFO] Job root.SBG_FASTA_Indices has started
[2018-01-25 13:59:20.407] [INFO] Pulling docker image images.sbgenomics.com/djordje_klisic/sbg-fasta-indices:1.0
[2018-01-25 13:59:20.408] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:20.429] [INFO] Running command line: python /opt/sbg-fasta-indices.py --dict --fai --REFERENCE /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-135908.146/root/SBG_FASTA_Indices/chr12.fasta
[2018-01-25 13:59:27.167] [INFO] Pulling docker image images.sbgenomics.com/mladenlsbg/fastqc:0.11.4
[2018-01-25 13:59:27.167] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:27.191] [INFO] Running command line: fastqc  --noextract --outdir . --threads 2 /home/biouser/AGBL_LABS/rabix/WGS_TEST/small_data/10049_R1.fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/small_data/10049_R2.fastq
[2018-01-25 13:59:30.332] [INFO] Job root.SBG_FASTA_Indices has completed
[2018-01-25 13:59:30.403] [INFO] Job root.SBG_Prepare_Intervals has started
[2018-01-25 13:59:30.413] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_prepare_intervals:1.0
[2018-01-25 13:59:30.413] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 13:59:30.445] [INFO] Running command line: python sbg_prepare_intervals.py --bed /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-135908.146/root/SBG_Prepare_Intervals/chr12.bed --fai /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-135908.146/root/SBG_FASTA_Indices/chr12.fasta.fai --mode 2
[2018-01-25 13:59:31.634] [ERROR] Failed to execute status command for root.SBG_Prepare_Intervals. Could not collect outputs.
org.rabix.executor.ExecutorException: Could not collect outputs.
    at org.rabix.executor.handler.impl.JobHandlerImpl.postprocess(JobHandlerImpl.java:318) ~[rabix-cli.jar:na]
    at org.rabix.executor.execution.command.StatusCommand.run(StatusCommand.java:52) ~[rabix-cli.jar:na]
    at org.rabix.executor.execution.JobHandlerCommand.run(JobHandlerCommand.java:51) [rabix-cli.jar:na]
    at org.rabix.executor.execution.JobHandlerRunnable.run(JobHandlerRunnable.java:58) [rabix-cli.jar:na]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_162]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_162]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_162]
Caused by: org.rabix.bindings.BindingException: org.rabix.bindings.sb.expression.SBExpressionException: Failed to evaluate outputEval.
    at org.rabix.bindings.sb.SBProcessor.postprocess(SBProcessor.java:146) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.SBBindings.postprocess(SBBindings.java:79) ~[rabix-cli.jar:na]
    at org.rabix.executor.handler.impl.JobHandlerImpl.postprocess(JobHandlerImpl.java:278) ~[rabix-cli.jar:na]
    ... 6 common frames omitted
Caused by: org.rabix.bindings.sb.expression.SBExpressionException: Failed to evaluate outputEval.
    at org.rabix.bindings.sb.helper.SBBindingHelper.evaluateOutputEval(SBBindingHelper.java:111) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.SBProcessor.collectOutput(SBProcessor.java:268) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.SBProcessor.collectOutputs(SBProcessor.java:164) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.SBProcessor.postprocess(SBProcessor.java:131) ~[rabix-cli.jar:na]
    ... 8 common frames omitted
Caused by: org.rabix.bindings.sb.expression.SBExpressionException: Failed evaluating expression {   
 content =  $self[0].contents.replace(/\0/g, '')
 content = content.replace('[','')
 content = content.replace(']','')
 content = content.replace(/\'/g, "")
 content = content.replace(/\s/g, '')
 content_arr = content.split(",")

 return content_arr

} .
    at org.rabix.bindings.sb.expression.javascript.SBExpressionJavascriptResolver.evaluate(SBExpressionJavascriptResolver.java:94) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.expression.SBExpressionResolver.evaluate(SBExpressionResolver.java:55) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.expression.SBExpressionResolver.evaluate(SBExpressionResolver.java:38) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.expression.helper.SBExpressionBeanHelper.evaluate(SBExpressionBeanHelper.java:44) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.helper.SBBindingHelper.evaluateOutputEval(SBBindingHelper.java:109) ~[rabix-cli.jar:na]
    ... 11 common frames omitted
Caused by: org.mozilla.javascript.EcmaError: TypeError: Cannot call method "replace" of undefined (script#2)
    at org.mozilla.javascript.ScriptRuntime.constructError(ScriptRuntime.java:3951) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.constructError(ScriptRuntime.java:3929) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.typeError(ScriptRuntime.java:3962) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.typeError2(ScriptRuntime.java:3981) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.undefCallError(ScriptRuntime.java:3998) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.getPropFunctionAndThisHelper(ScriptRuntime.java:2414) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.getPropFunctionAndThis(ScriptRuntime.java:2407) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.Interpreter.interpretLoop(Interpreter.java:1322) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.Interpreter.interpret(Interpreter.java:815) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.InterpretedFunction.call(InterpretedFunction.java:109) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:393) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.expression.javascript.SBExpressionContextFactory.doTopCall(SBExpressionContextFactory.java:54) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3282) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.InterpretedFunction.exec(InterpretedFunction.java:120) ~[rabix-cli.jar:na]
    at org.mozilla.javascript.Context.evaluateString(Context.java:1219) ~[rabix-cli.jar:na]
    at org.rabix.bindings.sb.expression.javascript.SBExpressionJavascriptResolver.evaluate(SBExpressionJavascriptResolver.java:74) ~[rabix-cli.jar:na]
    ... 15 common frames omitted
[2018-01-25 13:59:31.635] [INFO] Failed to execute status command for root.SBG_Prepare_Intervals. Could not collect outputs.
Failed to execute status command for root.SBG_Prepare_Intervals. Could not collect outputs.
gezthxbio commented 6 years ago

Fixed it by removing eval expression New error

[2018-01-25 15:14:35.409] [INFO] Running command line: python sbg_prepare_intervals.py --bed /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-151413.29/root/SBG_Prepare_Intervals/chr12.bed --fai /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-151413.29/root/SBG_FASTA_Indices/chr12.fasta.fai --mode 2
[2018-01-25 15:14:36.628] [INFO] Job root.SBG_Prepare_Intervals has completed
[2018-01-25 15:14:40.698] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has completed
[2018-01-25 15:14:41.645] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has completed
[2018-01-25 15:14:41.664] [INFO] Job root.SBG_Pair_FASTQs_by_Metadata has started
[2018-01-25 15:14:41.671] [INFO] Pulling docker image images.sbgenomics.com/nikola_jovanovic/sbg-pair-fastqs-by-metadata:v1
[2018-01-25 15:14:41.672] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-25 15:14:41.696] [INFO] Running command line: python pair_fastqs_by_metadata.py --fastq_list /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-151413.29/root/SBG_Pair_FASTQs_by_Metadata/10049_R1.fastq,/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-25-151413.29/root/SBG_Pair_FASTQs_by_Metadata/10049_R2.fastq --in_metafile job.json --out_metafile cwl.output.json
[2018-01-25 15:14:42.902] [INFO] Job root.SBG_Pair_FASTQs_by_Metadata failed with exit code 1. with message: Traceback (most recent call last):
  File "pair_fastqs_by_metadata.py", line 153, in <module>
    main()
  File "pair_fastqs_by_metadata.py", line 142, in main
    tuple_list = group_inputs(file_list)
  File "pair_fastqs_by_metadata.py", line 83, in group_inputs
    files = sorted([x for x in inp], key=key_getter)
  File "pair_fastqs_by_metadata.py", line 57, in make_rg_id
    if key in input_meta:
TypeError: argument of type 'NoneType' is not iterable

Job root.SBG_Pair_FASTQs_by_Metadata failed with exit code 1. with message: Traceback (most recent call last):
  File "pair_fastqs_by_metadata.py", line 153, in <module>
    main()
  File "pair_fastqs_by_metadata.py", line 142, in main
    tuple_list = group_inputs(file_list)
  File "pair_fastqs_by_metadata.py", line 83, in group_inputs
    files = sorted([x for x in inp], key=key_getter)
  File "pair_fastqs_by_metadata.py", line 57, in make_rg_id
    if key in input_meta:
TypeError: argument of type 'NoneType' is not iterable

I have created a metadata file

{
        "fastq": [
            {
                "name": "10049_R1.fastq",
                "metadata": {
                    "paired_end": "1",
                    "quality_scale": "illumina18",
                    "sample_id": "10049",
                    "platform": "Illumina-HiSeq-XTen",
                    "experimental_strategy": "WGS",
                },
                "class": "File",
                "path": "small_data/10049_R1.fastq"
            },
            {
                "name": "10049_R2.fastq",
                "metadata": {
                    "paired_end": "2",
                    "quality_scale": "illumina18",
                    "sample_id": "10049",
                    "platform": "Illumina-HiSeq-XTen",
                    "experimental_strategy": "WGS",
                },
                "class": "File",
                "path": "small_data/10049_R2.fastq"
            }
        ]
}

how do I give this json file as input to cwl file?

milos-ljubinkovic commented 6 years ago

Put it before the first -- in the command line 

/home/biouser/bin/rabix-cli-1.0.4/rabix wholegs.cwl /path/to/inputs.json -- --dbsnp /home/biouser/AGBL_LABS/GATK_FILES/dbsnp_138.hg19.vcf \
        --hapmap /home/biouser/AGBL_LABS/GATK_FILES/hapmap_3.3.hg19.sites.vcf \
        --known_indels_1000g_bqsr /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.indels.hg19.sites.vcf \
        --mills /home/biouser/AGBL_LABS/GATK_FILES/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
        --omni_1000g /home/biouser/AGBL_LABS/GATK_FILES/1000G_omni2.5.hg19.sites.vcf \
        --phase1_snp_1000g /home/biouser/AGBL_LABS/GATK_FILES/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
        --reference chr12.fasta \
        --intervals_file chr12.bed \
        --memory_per_job 5120MB \
        --threads 15
gezthxbio commented 6 years ago

Executed new error due to file not found

[2018-01-27 11:57:42.660] [INFO] Job root.SBG_Untar_fasta has started
[2018-01-27 11:57:42.660] [INFO] Job root.SBG_Prepare_VQSR_HapMap has started
[2018-01-27 11:57:42.660] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has started
[2018-01-27 11:57:42.660] [INFO] Job root.SBG_Prepare_VQSR_1000G has started
[2018-01-27 11:57:42.660] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has started
[2018-01-27 11:57:42.662] [INFO] Job root.SBG_Prepare_VQSR_Omni has started
[2018-01-27 11:57:42.662] [INFO] Job root.SBG_Prepare_VQSR_dbSNP has started
[2018-01-27 11:57:42.662] [INFO] Job root.FastQC has started
[2018-01-27 11:57:42.662] [INFO] Job root.SBG_Prepare_VQSR_Mills has started
[2018-01-27 11:57:42.662] [INFO] Job root.BWA_INDEX has started
[2018-01-27 11:57:43.268] [INFO] Pulling docker image ubuntu:14.04
[2018-01-27 11:57:43.275] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-27 11:57:43.921] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-27 11:57:43.989] [INFO] Pulling docker image ubuntu:14.04
[2018-01-27 11:57:43.990] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-27 11:57:44.159] [INFO] Pulling docker image ubuntu:14.04
[2018-01-27 11:57:44.160] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-27 11:57:44.180] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-27 11:57:44.185] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-27 11:57:45.568] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/bwa:0.7.13
[2018-01-27 11:57:45.569] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:45.620] [INFO] Running command line: /opt/bwa-0.7.13/bwa index chr12.fasta       ; tar -cf chr12.fasta.tar chr12.fasta *.amb *.ann *.bwt *.pac *.sa
[2018-01-27 11:57:45.640] [INFO] Pulling docker image images.sbgenomics.com/markop/sbg-decompressor:1.0
[2018-01-27 11:57:45.640] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:45.873] [INFO] Running command line: echo Passing input file
[2018-01-27 11:57:46.404] [INFO] Job root.SBG_Prepare_VQSR_Mills has completed
[2018-01-27 11:57:47.737] [INFO] Job root.SBG_Prepare_VQSR_Omni has completed
[2018-01-27 11:57:48.293] [INFO] Job root.SBG_Prepare_VQSR_HapMap has completed
[2018-01-27 11:57:50.761] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-27 11:57:50.761] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:50.789] [INFO] Running command line: echo No conversion
[2018-01-27 11:57:51.141] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_quality_scale_adjuster:2.0
[2018-01-27 11:57:51.141] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:51.169] [INFO] Running command line: echo No conversion
[2018-01-27 11:57:52.323] [INFO] Job root.SBG_Untar_fasta has completed
[2018-01-27 11:57:52.375] [INFO] Job root.SBG_FASTA_Indices has started
[2018-01-27 11:57:52.380] [INFO] Pulling docker image images.sbgenomics.com/djordje_klisic/sbg-fasta-indices:1.0
[2018-01-27 11:57:52.381] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:52.401] [INFO] Running command line: python /opt/sbg-fasta-indices.py --dict --fai --REFERENCE /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_FASTA_Indices/chr12.fasta
[2018-01-27 11:57:59.067] [INFO] Pulling docker image images.sbgenomics.com/mladenlsbg/fastqc:0.11.4
[2018-01-27 11:57:59.068] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:57:59.092] [INFO] Running command line: fastqc  --noextract --outdir . --threads 2 /home/biouser/AGBL_LABS/rabix/WGS_TEST/small_data/10049_R1.fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/small_data/10049_R2.fastq
[2018-01-27 11:58:02.292] [INFO] Job root.SBG_FASTA_Indices has completed
[2018-01-27 11:58:02.379] [INFO] Job root.SBG_Prepare_Intervals has started
[2018-01-27 11:58:02.388] [INFO] Pulling docker image images.sbgenomics.com/bogdang/sbg_prepare_intervals:1.0
[2018-01-27 11:58:02.389] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:58:02.419] [INFO] Running command line: python sbg_prepare_intervals.py --bed /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_Prepare_Intervals/chr12.bed --fai /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_FASTA_Indices/chr12.fasta.fai --mode 2
[2018-01-27 11:58:03.640] [INFO] Job root.SBG_Prepare_Intervals has completed
[2018-01-27 11:58:07.521] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.2 has completed
[2018-01-27 11:58:08.159] [INFO] Job root.SBG_FASTQ_Quality_Adjuster.1 has completed
[2018-01-27 11:58:08.176] [INFO] Job root.SBG_Pair_FASTQs_by_Metadata has started
[2018-01-27 11:58:08.184] [INFO] Pulling docker image images.sbgenomics.com/nikola_jovanovic/sbg-pair-fastqs-by-metadata:v1
[2018-01-27 11:58:08.185] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:58:08.207] [INFO] Running command line: python pair_fastqs_by_metadata.py --fastq_list /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_Pair_FASTQs_by_Metadata/10049_R1.fastq,/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_Pair_FASTQs_by_Metadata/10049_R2.fastq --in_metafile job.json --out_metafile cwl.output.json
[2018-01-27 11:58:22.215] [INFO] Pulling docker image ubuntu:14.04
[2018-01-27 11:58:22.216] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-27 11:58:22.234] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-27 11:58:24.760] [INFO] Job root.SBG_Pair_FASTQs_by_Metadata has completed
[2018-01-27 11:58:39.214] [INFO] Pulling docker image ubuntu:14.04
[2018-01-27 11:58:39.214] [ERROR] Could not find auth config for https://index.docker.io/v1/. Returning empty builder
[2018-01-27 11:58:39.231] [INFO] Running command line: echo Preparing VQSR Resources
[2018-01-27 11:58:50.616] [INFO] Job root.FastQC has completed
[2018-01-27 11:58:50.678] [INFO] Job root.SBG_Html2b64.1 has started
[2018-01-27 11:58:50.678] [INFO] Job root.SBG_Html2b64.2 has started
[2018-01-27 11:58:50.683] [INFO] Pulling docker image images.sbgenomics.com/mladenlsbg/sbg-html-to-b64:1.0.1
[2018-01-27 11:58:50.683] [INFO] Pulling docker image images.sbgenomics.com/mladenlsbg/sbg-html-to-b64:1.0.1
[2018-01-27 11:58:50.684] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:58:50.684] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 11:58:50.710] [INFO] Running command line: python /opt/sbg_html_to_b64.py --input /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/FastQC/10049_R2_fastqc.zip
[2018-01-27 11:58:50.713] [INFO] Running command line: python /opt/sbg_html_to_b64.py --input /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/FastQC/10049_R1_fastqc.zip
[2018-01-27 11:58:51.917] [INFO] Job root.SBG_Html2b64.1 has completed
[2018-01-27 11:58:52.072] [INFO] Job root.SBG_Html2b64.2 has completed
[2018-01-27 11:59:36.328] [INFO] Job root.SBG_Prepare_VQSR_1000G has completed
[2018-01-27 12:00:26.249] [INFO] Job root.SBG_Prepare_VQSR_dbSNP has completed
[2018-01-27 12:07:48.168] [INFO] Job root.BWA_INDEX has completed
[2018-01-27 12:07:48.296] [INFO] Job root.BWA_MEM_Bundle_0_7_13.1 has started
[2018-01-27 12:07:48.315] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/bwa:0.7.13
[2018-01-27 12:07:48.316] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-27 12:07:48.399] [INFO] Running command line:  tar -xf chr12.fasta.tar ;  /opt/bwa-0.7.13/bwa mem -M -R '@RG\tID:1\tPL:Illumina-HiSeq-XTen\tSM:10049' -t 30 chr12.fasta /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_Pair_FASTQs_by_Metadata/10049_R1.fastq /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/SBG_Pair_FASTQs_by_Metadata/10049_R2.fastq | /opt/samblaster/samblaster -i /dev/stdin -o /dev/stdout | /opt/sambamba_v0.6.0 view -t 30 --filter 'not secondary_alignment' -f bam -l 0 -S /dev/stdin | /opt/sambamba_v0.6.0 sort -t 30 -m 18GiB --tmpdir ./ -o 10049_R.bam -l 5 /dev/stdin ;declare -i pipe_statuses=(\${PIPESTATUS[*]});len=\${#pipe_statuses[@]};declare -i tot=0;echo \${pipe_statuses[*]};for (( i=0; i<\${len}; i++ ));do if [ \${pipe_statuses[\$i]} -ne 0 ];then tot=\${pipe_statuses[\$i]}; fi;done;if [ \$tot -ne 0 ]; then >&2 echo Error in piping. Pipe statuses: \${pipe_statuses[*]};fi; if [ \$tot -ne 0 ]; then false;fi
[2018-01-27 12:09:56.184] [INFO] Job root.BWA_MEM_Bundle_0_7_13.1 has completed
[2018-01-27 12:09:56.340] [INFO] Job root.GATK_RealignerTargetCreator.2 has started
[2018-01-27 12:09:56.340] [INFO] Job root.Sambamba_View.1 has started
[2018-01-27 12:09:56.340] [INFO] Job root.GATK_RealignerTargetCreator.1 has started
[2018-01-27 12:09:56.373] [ERROR] Execution failed for root.Sambamba_View.1. Failed to create a container: class java.io.IOException : File /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai doesn't exist
org.rabix.executor.container.ContainerException: Failed to create a container: class java.io.IOException : File /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai doesn't exist
    at org.rabix.executor.container.impl.DockerContainerHandler.start(DockerContainerHandler.java:295) ~[rabix-cli.jar:na]
    at org.rabix.executor.handler.impl.JobHandlerImpl.start(JobHandlerImpl.java:176) ~[rabix-cli.jar:na]
    at org.rabix.executor.execution.command.StartCommand.run(StartCommand.java:32) ~[rabix-cli.jar:na]
    at org.rabix.executor.execution.JobHandlerCommand.run(JobHandlerCommand.java:51) [rabix-cli.jar:na]
    at org.rabix.executor.execution.JobHandlerRunnable.run(JobHandlerRunnable.java:58) [rabix-cli.jar:na]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_162]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_162]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_162]
Caused by: java.io.IOException: File /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai doesn't exist
    at org.rabix.executor.container.impl.DockerContainerHandler.createBind(DockerContainerHandler.java:303) ~[rabix-cli.jar:na]
    at org.rabix.executor.container.impl.DockerContainerHandler.start(DockerContainerHandler.java:215) ~[rabix-cli.jar:na]
    ... 7 common frames omitted
[2018-01-27 12:09:56.374] [INFO] Execution failed for root.Sambamba_View.1. Failed to create a container: class java.io.IOException : File /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai doesn't exist
Execution failed for root.Sambamba_View.1. Failed to create a container: class java.io.IOException : File /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai doesn't exist

In BWA_MEM_Bundle_0_7_13/1/cwl.output.json file I see a file 10049_R.bai which is not present

{
  "aligned_reads" : {
    "checksum" : "sha1$356761f699bbe45334cb61c4730536a7ec2baa32",
    "class" : "File",
    "metadata" : {
      "experimental_strategy" : "WGS",
      "platform" : "Illumina-HiSeq-XTen",
      "quality_scale" : "illumina18",
      "reference_genome" : "chr12",
      "sample_id" : "10049"
    },
    "name" : "10049_R.bam",
    "path" : "/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bam",
    "secondaryFiles" : [ {
      "checksum" : "sha1$14e4c6aff2c9ddcec57db546a03756e8ebfd4586",
      "class" : "File",
      "dirname" : "/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1",
      "location" : "file:///home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bam.bai",
      "name" : "10049_R.bam.bai",
      "path" : "/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bam.bai",
      "size" : 933096
    }, {
      "class" : "File",
      "dirname" : "/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1",
     "location" : "file:///home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai",
      "name" : "10049_R.bai",
      "path" : "/home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-27-115740.222/root/BWA_MEM_Bundle_0_7_13/1/10049_R.bai"
    } ],
    "size" : 654534144
  }
}
milos-ljubinkovic commented 6 years ago

Will probably work with the release I updated yesterday. Some code around secondary files was changed and caused issues with apps that declare secondary files but don't create them.

gezthxbio commented 6 years ago

Everything went fine till last step

[2018-01-30 09:28:43.314] [INFO] Job root.GATK_ApplyRecalibration_1 has completed
[2018-01-30 09:28:43.359] [INFO] Job root.SnpEff has started
[2018-01-30 09:28:50.900] [INFO] Pulling docker image images.sbgenomics.com/vladimirk/snpeff:4.2
[2018-01-30 09:28:50.901] [ERROR] Could not find auth config for images.sbgenomics.com. Returning empty builder
[2018-01-30 09:28:51.007] [INFO] Running command line: unzip -o /home/biouser/bin/snpEff_latest_core/database/snpEff_v4_3_GRCh37.75.zip -d /opt/snpEff ; java -Xmx10240M -jar /opt/snpEff/snpEff.jar -nodownload -noLog -o vcf -t snpEff_v4_3_GRCh37.75 /home/biouser/AGBL_LABS/rabix/WGS_TEST/wgs58.cwl-2018-01-29-090251.412/root/GATK_ApplyRecalibration_1/Sample_NA12878.Library_Unknown.Platform_Unit_Unknown.combined.recalibrated.recalibrated.vcf > Sample_NA12878.Library_Unknown.Platform_Unit_Unknown.combined.recalibrated.recalibrated.snpEff_annotated.vcf
[2018-01-30 09:28:58.842] [INFO] Job root.SnpEff failed with exit code 255. with message: java.lang.RuntimeException: Property: 'snpEff_v4_3_GRCh37.75.genome' not found
        at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:955)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

Job root.SnpEff failed with exit code 255. with message: java.lang.RuntimeException: Property: 'snpEff_v4_3_GRCh37.75.genome' not found
        at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:955)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

We downloaded snpeff db from here.

vladimirkovacevic commented 6 years ago

SnpEff tool requires the name of the database file be the same as its library for that reference genome. Because of that snpEff_v4_3_GRCh37.75.zip should be renamed to GRCh37.75.zip