Strange error message when trying to re-launch failures

Hello Terra team,

 

I got this error message when trying to relaunch failed workflows for the getzlab/CGA_WES_Characterization_Pipeline_v0.1_Dec2018/2 pipeline:

 

Error rerunning failed workflows
Error 404: getzlab/CGA_WES_Characterization_Pipeline_v0.1_Dec2018_p4CWVc2pWLY does not exist in SlickWorkspaceContext(Workspace(broad-firecloud-cptac,CPTAC-3_20190717_LUAD_DS_Test,8e198fb6-e778-4fde-a926-09183b437175,fc-secure-8e198fb6-e778-4fde-a926-09183b437175,Some(8e198fb6-e778-4fde-a926-09183b437175),2019-07-17T15:55:09.626Z,2019-07-19T18:26:30.755Z,birger@broadinstitute.org,Map(AttributeName(default,KGENOMES_MUTECT_PON) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/pon/mutect/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf), AttributeName(default,ref_fasta_fai) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.fasta.fai), AttributeName(default,VEP_ZIP_FILE) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/my_dot_vep.zip), AttributeName(default,MUT_CATEGORIES) -> AttributeString(gs://getzlab-workflows-reference_files-oa/categs.txt), AttributeName(default,DB_SNP_VCF_IDX) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/dbsnp_138.b37.vcf.gz.tbi), AttributeName(default,ref_fasta) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.fasta), AttributeName(default,ONCO_TARBALL) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/oncotator_v1_ds_Jan262014.tar.gz), AttributeName(default,HG38_REF_FASTA) -> AttributeString(gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta), AttributeName(default,HAP_DB_FOR_CC) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.haplotype_database.txt), AttributeName(default,ACNV_PON) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/pon/gatk_cnv/open_access_pon_from_1000g.pon), AttributeName(default,HLA_FASTA) -> AttributeString(gs://cga_pipeline_reference/formatted_ABC_gen.fa), AttributeName(default,ILLUMINA_BAIT_INTERVALS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/ice/whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.baits.interval_list), AttributeName(default,HG19_TARBALL) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/annotation.db.ucsc.hg19.tar), AttributeName(default,CYTO_BAND) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/cytoBand.txt), AttributeName(default,READ_GROUP_BLACKLIST) -> AttributeString(gs://getzlab-workflows-reference_files-oa/read_group_blacklist.v1.txt), AttributeName(default,AGILENT_BAIT_INTERVALS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/agilent/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list), AttributeName(default,ref_ann) -> AttributeString(gs://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.64.ann), AttributeName(default,COMMON_VARIANTS_1000_GENOMES) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/1000genomes.common_variants.minor_allele_freq_5_percent.multi_allelic_sites_removed.variant_key.tsv), AttributeName(default,common_sites) -> AttributeString(gs://gatk-test-data/cnv/somatic/common_snps.interval_list), AttributeName(default,COSMIC_VCF) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/hg19_cosmic_v54_120711.vcf), AttributeName(default,intervals) -> AttributeString(gs://gatk-test-data/cnv/somatic/ice_targets.tsv.interval_list), AttributeName(default,big_cnv_blacklist) -> AttributeString(gs://gatk-best-practices/somatic-b37/CNV_and_centromere_blacklist.hg19.list), AttributeName(default,REF_FASTA) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.fasta), AttributeName(default,gatk_docker) -> AttributeString(us.gcr.io/broad-gatk/gatk:4.1.1.0), AttributeName(default,MUTECT_FC_INTERVALS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/panel_100_genes.interval_list), AttributeName(default,ref_alt) -> AttributeString(gs://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.alt), AttributeName(default,CGA_PIPELINE_CONFIG) -> AttributeString(gs://fc-secure-188f6b81-f211-48f2-b2da-2f7897edbada/cga_pipeline_config_optional_parameters.json), AttributeName(default,REF_FASTA_BWT) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.bwt), AttributeName(default,ACNV_ICE_FFPE_PON) -> AttributeString(gs://pon_for_production_cga_pipeline/PON_CNV/ice_gatk4_ffpe.pon), AttributeName(default,ACNV_PON_cfDNA) -> AttributeString(gs://private_reference_files/all_with_normal_for_pon.acnv.pon), AttributeName(default,description) -> AttributeString(), AttributeName(default,ONCO_TX_OVERRIDE_LIST) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/oncotator/tx_exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt), AttributeName(default,DUPLICATE_HUGO_SYMBOL) -> AttributeString(gs://cga_pipeline_reference/duplicate_hugo_symbols.txt), AttributeName(default,STRELKA_CONFIG) -> AttributeString(gs://getzlab-workflows-config_files/CGA_WES_Characterization/v0.1/strelka_config_bwa_cga_exome.ini), AttributeName(default,ploidy_priors) -> AttributeString(gs://fc-secure-779a9f8e-6c05-4b43-bf50-9b479469898f/contig_ploidy_prior_hg19.tsv), AttributeName(default,SNP6BED) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/SNP6.hg19.interval_list), AttributeName(default,EMPTY_MAF) -> AttributeString(gs://fc-secure-e84f3ca1-738e-45c7-a29a-bdbd78684d0f/empty_maf.maf), AttributeName(default,get_CN_RScript) -> AttributeString(gs://fc-secure-7cb116e5-ed44-4e2f-955c-f1b1a899fc6d/get_CN_Absolute.R), AttributeName(default,GENE_MAPPING) -> AttributeString(gs://cga_pipeline_reference/gene_id_name_mapping.txt), AttributeName(default,UCSC_ANNOTATION_DB) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/annotation.db.ucsc.hg19.tar), AttributeName(default,LUAD_CNV_PON_DS) -> AttributeString(gs://fc-secure-8e198fb6-e778-4fde-a926-09183b437175/743c8076-13b3-4d32-8d41-f1b4778ad0c4/CNVSomaticPanelWorkflow/3dff39b1-2098-49bd-b641-794343839a82/call-CreateReadCountPanelOfNormals/attempt-2/wes-do-gc.pon.hdf5), AttributeName(default,REF_FASTA_IDX) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.fasta.fai), AttributeName(default,GATK4_JAR) -> AttributeString(gs://getzlab-workflows-reference_files-oa/gatk-package-4.0.5.1-local.jar), AttributeName(default,AGILENT_TARGET_INTERVALS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/agilent/whole_exome_agilent_1.1_refseq_plus_3_boosters_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list), AttributeName(default,TOKEN_PON_MAKER_CONFIG) -> AttributeString(gs://getzlab-workflows-config_files/CGA_Token_PoN_Maker/v0.1/token_pon_maker_config_optional_parameters.json), AttributeName(default,RSEM_REFERENCE) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/rna-seq/rsem_reference_v19.tar.gz), AttributeName(default,GATK_PROTECTED_JAR) -> AttributeString(gs://getzlab-workflows-reference_files-oa/gatk-protected.jar), AttributeName(default,discoverableByGroups) -> AttributeString([]), AttributeName(default,DB_SNP_VCF) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/dbsnp_138.b37.vcf.gz), AttributeName(default,HAP_MAP_VCF) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/hg19_population_stratified_af_hapmap_3.3.fixed.vcf), AttributeName(default,ref_fasta_dict) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.dict), AttributeName(default,BLAT_REALIGNER_HG19_BIT) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/hg19.2bit), AttributeName(default,MAF_PON_FILTER_LIST) -> AttributeString(gs://fc-secure-e84f3ca1-738e-45c7-a29a-bdbd78684d0f/maf_pon_filter_pon_objects_list_tcga_ice.tsv), AttributeName(default,ACNV_PON_ICE) -> AttributeString(gs://pon_for_production_cga_pipeline/PON_CNV/ice_rcs_eval.v1.pd250.spark.pon), AttributeName(default,REF_FASTA_AMB) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.amb), AttributeName(default,HG38_REF_FASTA_IDX) -> AttributeString(gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai), AttributeName(default,REF_FASTA_ANN) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.ann), AttributeName(default,GENES_GTF) -> AttributeString(gs://cga_pipeline_reference/gencode.v19.genes.v7.patched_contigs.gtf), AttributeName(default,GOOD_HETS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/only_very_good_hets.tsv), AttributeName(default,LUAD_CN_PoN_CPTAC3) -> AttributeString(gs://fc-secure-72d0da1f-9577-4ea6-b827-acf988e2d641/a6240d73-8744-41ce-977f-5eff2162b331/CNVSomaticPanelWorkflow/f770561f-66aa-46cf-b51d-e9b484fcbfbe/call-CreateReadCountPanelOfNormals/wes-do-gc.pon.hdf5), AttributeName(default,STAR_INDEX) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/rna-seq/star_index_v19_oh75.tar.gz), AttributeName(default,REGION_FILE) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/capture_region_list), AttributeName(default,INDEL_VCF_IDX) -> AttributeString(gs://broad-references/hg19/v0/Homo_sapiens_assembly19.known_indels_20120518.vcf.idx), AttributeName(default,REF_FASTA_DICT) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/Homo_sapiens_assembly19.dict), AttributeName(default,REF_FASTA_PAC) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.pac), AttributeName(default,CAP_NORM_DB_ZIP) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/capture_normals_db_hg19_v4.zip), AttributeName(default,INDEL_VCF) -> AttributeString(gs://broad-references/hg19/v0/Homo_sapiens_assembly19.known_indels_20120518.vcf), AttributeName(default,EXAC_PICKLE) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/exac.pickle_high_af), AttributeName(default,REF_FASTA_SA) -> AttributeString(gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.sa), AttributeName(default,ILLUMINA_TARGET_INTERVALS) -> AttributeString(gs://getzlab-workflows-reference_files-oa/hg19/ice/whole_exome_illumina_coding_v1_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list)),false))
Source: rawls

 

I am not sure what this error message means.

 

Thank you for your help,

Luda

Comments

3 comments

  • Comment author
    Liudmila Elagina

    Just a side note, I was able to launch the same workflow regularly.  Why would I get an error when trying to launch through the "Relaunch failures" option?

     

    Thank you

    0
  • Comment author
    Sushma Chaluvadi

    Hi Luda,

    So sorry for the delay on this! Can you check attempting to Relaunch Failures on that same one again? I wonder if it was related to a bug we found on Friday which was fixed today. I suspect it is not the same but it would be worth checking just to eliminate it as a possibility.

    Sushma

    0
  • Comment author
    Allie Hajian

    Note that reference data files are no longer located in the "gs://broad-references/" bucket but have been moved to gs://gcp-public-data--broad-references, hosted by Google. 

    0

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