[2024-01-24 14:05:44,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:44,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:44,431] [INFO] DQC Reference Directory: /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference
[2024-01-24 14:05:45,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:45,838] [INFO] Task started: Prodigal
[2024-01-24 14:05:45,838] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2e45aa7-1c2f-4acb-aa9d-8c6e0feed17a/GCF_030506305.1_ASM3050630v1_genomic.fna.gz | prodigal -d GCF_030506305.1_ASM3050630v1_genomic.fna/cds.fna -a GCF_030506305.1_ASM3050630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:06,906] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:06,907] [INFO] Task started: HMMsearch
[2024-01-24 14:06:06,907] [INFO] Running command: hmmsearch --tblout GCF_030506305.1_ASM3050630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/reference_markers.hmm GCF_030506305.1_ASM3050630v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:07,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:07,196] [INFO] Found 6/6 markers.
[2024-01-24 14:06:07,245] [INFO] Query marker FASTA was written to GCF_030506305.1_ASM3050630v1_genomic.fna/markers.fasta
[2024-01-24 14:06:07,246] [INFO] Task started: Blastn
[2024-01-24 14:06:07,246] [INFO] Running command: blastn -query GCF_030506305.1_ASM3050630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/reference_markers.fasta -out GCF_030506305.1_ASM3050630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:07,854] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:07,858] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:07,858] [INFO] Target genome list was writen to GCF_030506305.1_ASM3050630v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:07,875] [INFO] Task started: fastANI
[2024-01-24 14:06:07,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2e45aa7-1c2f-4acb-aa9d-8c6e0feed17a/GCF_030506305.1_ASM3050630v1_genomic.fna.gz --refList GCF_030506305.1_ASM3050630v1_genomic.fna/target_genomes.txt --output GCF_030506305.1_ASM3050630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:25,413] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:25,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:25,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:25,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:25,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 14:06:25,416] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2024-01-24 14:06:25,417] [INFO] DFAST Taxonomy check result was written to GCF_030506305.1_ASM3050630v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:25,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:25,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:25,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/checkm_data
[2024-01-24 14:06:25,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:25,470] [INFO] Task started: CheckM
[2024-01-24 14:06:25,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030506305.1_ASM3050630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030506305.1_ASM3050630v1_genomic.fna/checkm_input GCF_030506305.1_ASM3050630v1_genomic.fna/checkm_result
[2024-01-24 14:07:22,662] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:22,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:22,681] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:22,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:22,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030506305.1_ASM3050630v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:22,682] [INFO] Task started: Blastn
[2024-01-24 14:07:22,682] [INFO] Running command: blastn -query GCF_030506305.1_ASM3050630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf74b55aa-c72e-4bc6-9bfd-2ee6cf4eaa77/dqc_reference/reference_markers_gtdb.fasta -out GCF_030506305.1_ASM3050630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:23,502] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:23,506] [INFO] Selected 34 target genomes.
[2024-01-24 14:07:23,506] [INFO] Target genome list was writen to GCF_030506305.1_ASM3050630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:23,538] [INFO] Task started: fastANI
[2024-01-24 14:07:23,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2e45aa7-1c2f-4acb-aa9d-8c6e0feed17a/GCF_030506305.1_ASM3050630v1_genomic.fna.gz --refList GCF_030506305.1_ASM3050630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030506305.1_ASM3050630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:48,165] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:48,167] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:48,167] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
--------------------------------------------------------------------------------
[2024-01-24 14:07:48,169] [INFO] GTDB search result was written to GCF_030506305.1_ASM3050630v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:48,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:48,171] [INFO] DFAST_QC result json was written to GCF_030506305.1_ASM3050630v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:48,172] [INFO] DFAST_QC completed!
[2024-01-24 14:07:48,172] [INFO] Total running time: 0h2m4s