Nothing seems to have failed, but the presence of the error in my log is worrying.
Here's my JES log:
2016/02/04 19:34:48 I: Switching to status: start(n1-standard-1)
2016/02/04 19:37:06 I: Switching to status: pulling-image
2016/02/04 19:38:10 I: Writing new Docker configuration file
2016/02/04 19:38:10 I: Pulling image "dlivitzbroad/cnvvdev"
2016/02/04 19:39:42 I: Pulled image "dlivitzbroad/cnvvdev" successfully.
2016/02/04 19:39:42 I: Switching to status: localizing-files
2016/02/04 19:40:46 I: Docker file /cromwell_root/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta maps to host location /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta.
2016/02/04 19:40:46 I: Copying gs://fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta to /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta
2016/02/04 19:41:50 I: Docker file /cromwell_root/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta.fai maps to host location /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta.fai.
2016/02/04 19:41:50 I: Copying gs://fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta.fai to /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.fasta.fai
2016/02/04 19:41:51 I: Docker file /cromwell_root/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets_germline_copy_number_variants_X_Y_removed.bed maps to host location /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets_germline_copy_number_variants_X_Y_removed.bed.
2016/02/04 19:41:51 I: Copying gs://fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets_germline_copy_number_variants_X_Y_removed.bed to /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets_germline_copy_number_variants_X_Y_removed.bed
2016/02/04 19:41:53 I: Docker file /cromwell_root/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam maps to host location /mnt/local-disk/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam.
2016/02/04 19:41:53 I: Copying gs://360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam to /mnt/local-disk/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam
2016/02/04 19:59:23 I: Docker file /cromwell_root/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam.bai maps to host location /mnt/local-disk/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam.bai.
2016/02/04 19:59:23 I: Copying gs://360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam.bai to /mnt/local-disk/360ee3ad-adef-44ee-82c2-52f9a5e7f99a/tcga/GBM/DNA/WXS/BI/ILLUMINA/C484.TCGA-28-2513-10A-01D-1494-08.6.bam.bai
2016/02/04 19:59:25 I: Docker file /cromwell_root/exec.sh maps to host location /mnt/local-disk/exec.sh.
2016/02/04 19:59:25 I: Copying gs://fc-4d0f16cf-65e3-410f-b84e-02d232fd30cb/c390865d-d8fd-46a0-9898-1467b2a9349c/gatk_cnv_coverage_wkfl/017d619f-99d5-418a-9c6d-7ea38e8fc8a4/call-gatk_cnv_coverage/exec.sh to /mnt/local-disk/exec.sh
2016/02/04 19:59:26 I: Docker file /cromwell_root/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.dict maps to host location /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.dict.
2016/02/04 19:59:26 I: Copying gs://fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.dict to /mnt/local-disk/fc-c6d7d374-d16a-4f47-a60b-597263a1d885/ref_data/Homo_sapiens_assembly19.dict
2016/02/04 19:59:31 I: Done copying files.
2016/02/04 19:59:31 I: Switching to status: running-docker
2016/02/04 20:00:34 I: Setting these data volumes on the docker container: [-v /tmp/ggp-876206253:/tmp/ggp-876206253 -v /mnt/local-disk:/cromwell_root]
2016/02/04 20:19:48 I: Switching to status: delocalizing-files
2016/02/04 20:19:49 E: update status to "run" failed: exit status 1: ERROR: (gcloud.compute.instances.add-metadata) There was a problem fetching the resource:
- Rate Limit Exceeded
2016/02/04 20:19:49 I: Docker file /cromwell_root/TCGA-28-2513-10A-01D-1494-08.coverage.tsv maps to host location /mnt/local-disk/TCGA-28-2513-10A-01D-1494-08.coverage.tsv.
2016/02/04 20:19:49 I: Copying /mnt/local-disk/TCGA-28-2513-10A-01D-1494-08.coverage.tsv to gs://fc-4d0f16cf-65e3-410f-b84e-02d232fd30cb/c390865d-d8fd-46a0-9898-1467b2a9349c/gatk_cnv_coverage_wkfl/017d619f-99d5-418a-9c6d-7ea38e8fc8a4/call-gatk_cnv_coverage/TCGA-28-2513-10A-01D-1494-08.coverage.tsv
2016/02/04 20:19:50 I: Docker file /cromwell_root/job.rc.txt maps to host location /mnt/local-disk/job.rc.txt.
2016/02/04 20:19:50 I: Copying /mnt/local-disk/job.rc.txt to gs://fc-4d0f16cf-65e3-410f-b84e-02d232fd30cb/c390865d-d8fd-46a0-9898-1467b2a9349c/gatk_cnv_coverage_wkfl/017d619f-99d5-418a-9c6d-7ea38e8fc8a4/call-gatk_cnv_coverage/job.rc.txt
2016/02/04 20:19:51 I: Docker file /cromwell_root/job.stderr.txt maps to host location /mnt/local-disk/job.stderr.txt.
2016/02/04 20:19:51 I: Copying /mnt/local-disk/job.stderr.txt to gs://fc-4d0f16cf-65e3-410f-b84e-02d232fd30cb/c390865d-d8fd-46a0-9898-1467b2a9349c/gatk_cnv_coverage_wkfl/017d619f-99d5-418a-9c6d-7ea38e8fc8a4/call-gatk_cnv_coverage/job.stderr.txt
2016/02/04 20:19:52 I: Docker file /cromwell_root/job.stdout.txt maps to host location /mnt/local-disk/job.stdout.txt.
2016/02/04 20:19:52 I: Copying /mnt/local-disk/job.stdout.txt to gs://fc-4d0f16cf-65e3-410f-b84e-02d232fd30cb/c390865d-d8fd-46a0-9898-1467b2a9349c/gatk_cnv_coverage_wkfl/017d619f-99d5-418a-9c6d-7ea38e8fc8a4/call-gatk_cnv_coverage/job.stdout.txt
2016/02/04 20:19:54 I: Done copying files.