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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

Error response from daemon: No such container: spritz-615926720 #232

Closed animesh closed 1 year ago

animesh commented 1 year ago

Describing the issue

I am trying to run the example U2OS but facing "Error response from daemon: No such container: spritz-615926720" , detail log following

aa9e8496732d: Download complete
bc349dc43ca8: Download complete
4f4fb700ef54: Download complete
7a6db449b51b: Download complete
c89c10ffd84e: Download complete
26142b6b2c1e: Download complete
d0e88a31bdb3: Download complete
95da70874cd4: Download complete
377cc88d7c7e: Download complete
a7c07239fd15: Download complete
16f76cf3882a: Download complete
7a15ae76cb48: Download complete
b51904ca3834: Download complete
301aa5df7f62: Download complete
4dbbafe15647: Download complete
docker.io/smithlab/spritz:0.3.8
[?1h=Welcome to Spritz!
Testing analysis directory /app/spritz/results/
Using analysis directory /app/spritz/results/
Running `snakemake -j 6 --use-conda --conda-frontend mamba --configfile /app/spritz/results/config/config.yaml`.
Wildcard constraints in inputs are ignored.
Building DAG of jobs...
Creating conda environment envs/quant.yaml...
Downloading and installing remote packages.
Environment for envs/quant.yaml created (location: .snakemake/conda/a2cf4925)
Creating conda environment envs/spritzbase.yaml...
Downloading and installing remote packages.
Environment for envs/spritzbase.yaml created (location: .snakemake/conda/ce565c96)
Creating conda environment envs/isoforms.yaml...
Downloading and installing remote packages.
Environment for envs/isoforms.yaml created (location: .snakemake/conda/45a9cd02)
Creating conda environment envs/variants.yaml...
Downloading and installing remote packages.
Environment for envs/variants.yaml created (location: .snakemake/conda/180357af)
Creating conda environment envs/downloads.yaml...
Downloading and installing remote packages.
Environment for envs/downloads.yaml created (location: .snakemake/conda/5fe6c4ba)
Creating conda environment envs/align.yaml...
Downloading and installing remote packages.
Environment for envs/align.yaml created (location: .snakemake/conda/e361d902)
Creating conda environment envs/proteogenomics.yaml...
Downloading and installing remote packages.
Environment for envs/proteogenomics.yaml created (location: .snakemake/conda/47a7eecc)
Creating conda environment envs/sra.yaml...
Downloading and installing remote packages.
Environment for envs/sra.yaml created (location: .snakemake/conda/b68b2881)
Creating conda environment envs/default.yaml...
Downloading and installing remote packages.
Environment for envs/default.yaml created (location: .snakemake/conda/46c8395d)
Using shell: /bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job counts:
    count   jobs
    1   LongOrfs
    1   Predict
    1   all
    1   assemble_transcripts_sra_se
    1   base_recalibration
    1   blastp
    1   call_gvcf_varaints
    1   call_vcf_variants
    1   cdna_alignment_orf_to_genome_orf
    1   copy_gff3_to_snpeff
    1   custom_protein_xml
    1   dict_fa
    1   download_chromosome_mappings
    1   download_dbsnp_vcf
    1   download_ensembl_references
    1   download_protein_xml
    1   download_snpeff
    1   fastp_sra_se
    1   final_vcf_naming
    1   finish_isoform
    1   finish_isoform_variants
    1   finish_variants
    1   generate_reference_snpeff_database
    1   generate_snpeff_database
    1   gtf_file_to_cDNA_seqs
    1   gtf_to_alignment_gff3
    1   hisat2_align_bam_sra_se
    1   hisat2_group
    1   hisat2_mark
    1   hisat2_merge_bams
    1   hisat2_splice_sites
    1   hisat_genome
    1   index_ensembl_vcf
    1   index_fa
    1   make_gene_quant_dataframe_custom
    1   make_gene_quant_dataframe_ref
    1   make_isoform_quant_dataframe_custom
    1   make_isoform_quant_dataframe_ref
    1   makeblastdb
    1   merge_transcripts
    1   prefetch_sras_se
    1   prose
    1   quantify_ref_transcripts_sra_se
    1   quantify_transcripts_sra_se
    1   reference_protein_xml
    1   remove_exon_and_utr_information
    1   reorder_genome_fasta
    1   setup_ptmlist_links
    1   setup_transfer_mods
    1   split_n_cigar_reads
    1   split_sras_se
    1   transfer_modifications_isoformvariant
    1   transfer_modifications_variant
    1   variant_annotation_custom
    1   variant_annotation_ref
    1   variant_tmpdir
    56

ue Jul  4 13:33:11 2023]
rule setup_transfer_mods:
    input: ../SpritzModifications.dll
    output: ../resources/ptmlist.txt, ../resources/PSI-MOD.obo.xml
    log: ../resources/setup_transfer_mods.log
    jobid: 4
    benchmark: ../resources/setup_transfer_mods.benchmark


ue Jul  4 13:33:11 2023]
rule download_snpeff:
    output: ../resources/SnpEff/snpEff.config, ../resources/SnpEff/snpEff.jar, ../resources/SnpEff_4.3_SmithChemWisc_v2.zip
    log: ../resources/SnpEffInstall.log
    jobid: 6


ue Jul  4 13:33:11 2023]
rule download_protein_xml:
    output: ../resources/uniprot/Homo_sapiens.protein.xml.gz, ../resources/uniprot/Homo_sapiens.protein.fasta
    log: ../resources/uniprot/Homo_sapiens.protein.xml.gz.log
    jobid: 9
    benchmark: ../resources/uniprot/Homo_sapiens.protein.xml.gz.benchmark


ue Jul  4 13:33:11 2023]
rule variant_tmpdir:
    output: ../resources/tmp
    log: ../resources/tmpdir.log
    jobid: 29


ue Jul  4 13:33:11 2023]
rule download_chromosome_mappings:
    output: ../resources/ChromosomeMappings/GRCh38_UCSC2ensembl.txt
    log: ../resources/download_chromosome_mappings.log
    jobid: 16
    benchmark: ../resources/download_chromosome_mappings.benchmark


ue Jul  4 13:33:11 2023]
rule download_ensembl_references:
    output: ../resources/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa, ../resources/ensembl/Homo_sapiens.GRCh38.97.gff3, ../resources/ensembl/Homo_sapiens.GRCh38.pep.all.fa
    log: ../resources/ensembl/downloads.log
    jobid: 7
    benchmark: ../resources/ensembl/downloads.benchmark

Activating conda environment: /app/spritz/workflow/.snakemake/conda/5fe6c4ba
Activating conda environment: /app/spritz/workflow/.snakemake/conda/5fe6c4ba
Activating conda environment: /app/spritz/workflow/.snakemake/conda/180357af
Activating conda environment: /app/spritz/workflow/.snakemake/conda/ce565c96
Activating conda environment: /app/spritz/workflow/.snakemake/conda/5fe6c4ba
Activating conda environment: /app/spritz/workflow/.snakemake/conda/5fe6c4ba
ue Jul  4 13:33:12 2023]
Finished job 29.
1 of 56 steps (2%) done
ue Jul  4 13:33:13 2023]
Error in rule download_protein_xml:
    jobid: 9
    output: ../resources/uniprot/Homo_sapiens.protein.xml.gz, ../resources/uniprot/Homo_sapiens.protein.fasta
    log: ../resources/uniprot/Homo_sapiens.protein.xml.gz.log (check log file(s) for error message)
    conda-env: /app/spritz/workflow/.snakemake/conda/5fe6c4ba
    shell:
        (python scripts/get_proteome.py && python scripts/download_uniprot.py xml | gzip -c > ../resources/uniprot/Homo_sapiens.protein.xml.gz && python scripts/download_uniprot.py fasta > ../resources/uniprot/Homo_sapiens.protein.fasta) &> ../resources/uniprot/Homo_sapiens.protein.xml.gz.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

/bin/bash: line 1:  2162 Aborted                 dotnet ../SpritzModifications.dll --setup &> ../resources/setup_transfer_mods.log
ue Jul  4 13:33:15 2023]
Error in rule setup_transfer_mods:
    jobid: 4
    output: ../resources/ptmlist.txt, ../resources/PSI-MOD.obo.xml
    log: ../resources/setup_transfer_mods.log (check log file(s) for error message)
    conda-env: /app/spritz/workflow/.snakemake/conda/ce565c96
    shell:
        cd ../resources/ && dotnet ../SpritzModifications.dll --setup &> ../resources/setup_transfer_mods.log
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job setup_transfer_mods since they might be corrupted:
../resources/PSI-MOD.obo.xml
ue Jul  4 13:33:15 2023]
Finished job 16.
2 of 56 steps (4%) doneRemoving temporary output file ../resources/SnpEff_4.3_SmithChemWisc_v2.zip.
ue Jul  4 13:36:55 2023]
Finished job 6.
3 of 56 steps (5%) done
ue Jul  4 13:41:48 2023]
Finished job 7.
4 of 56 steps (7%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /app/spritz/workflow/.snakemake/log/2023-07-04T132836.941030.snakemake.log
[?1h=ERROR conda.cli.main_run:execute(49): `conda run dotnet SpritzCMD.dll --threads 6 --analysisDirectory=/app/spritz/results/ --reference=release-97,homo_sapiens,human,GRCh38 --analyzeVariants --analyzeIsoforms --doQuantification --sraAccessionSingleEnd=SRR629563` failed. (See above for error)
Error response from daemon: No such container: spritz-615926720
Done!

Screenshots image

Desktop information

jade15 commented 1 year ago

I had the same problem on different PCs tested.

acesnik commented 1 year ago

Thanks for the heads-up! I'll take a look

acesnik commented 1 year ago

Hi @animesh and @jade15, this is fixed now in version 0.3.10 (https://github.com/smith-chem-wisc/Spritz/releases/tag/0.3.10). The issue was a change in how programmatic downloads are done for UniProt.

For bookkeeping, changes were made here: https://github.com/smith-chem-wisc/Spritz/pull/231 https://github.com/smith-chem-wisc/Spritz/pull/233 https://github.com/smith-chem-wisc/mzLib/releases/tag/1.0.540

jade15 commented 1 year ago

That's awesome!!! Thank you so much. I'll try it right away!

animesh commented 1 year ago

Latest version seems to have worked past this issue 👍🏽 Just need to mention that i had to create and share F:\resources folder via docker, is it some hardcoded path?

acesnik commented 1 year ago

Good to hear! It looks like you're using the folder F:\TK\ from the other issue you posted, so it might be a notification because Docker is asking permission to use that drive. Yes, the resources folder is a hard-coded and usually automatically generated.