[2024-01-24 12:39:35,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,081] [INFO] DQC Reference Directory: /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference
[2024-01-24 12:39:36,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,280] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eec3e62-ae5c-4693-b535-a6358cdc053b/GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/cds.fna -a GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:41,977] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:41,977] [INFO] Task started: HMMsearch
[2024-01-24 12:39:41,978] [INFO] Running command: hmmsearch --tblout GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/reference_markers.hmm GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:42,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:42,240] [INFO] Found 6/6 markers.
[2024-01-24 12:39:42,272] [INFO] Query marker FASTA was written to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:39:42,273] [INFO] Task started: Blastn
[2024-01-24 12:39:42,273] [INFO] Running command: blastn -query GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/reference_markers.fasta -out GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:42,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:42,920] [INFO] Selected 24 target genomes.
[2024-01-24 12:39:42,921] [INFO] Target genome list was writen to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:39:42,939] [INFO] Task started: fastANI
[2024-01-24 12:39:42,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eec3e62-ae5c-4693-b535-a6358cdc053b/GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna.gz --refList GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:55,190] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:55,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:55,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:55,200] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:55,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:55,201] [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
Acetitomaculum ruminis	strain=DSM 5522	GCA_900112085.1	2382	2382	type	True	100.0	994	999	95	conclusive
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	77.9283	56	999	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	75.4277	55	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:55,203] [INFO] DFAST Taxonomy check result was written to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:39:55,204] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:55,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:55,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/checkm_data
[2024-01-24 12:39:55,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:55,238] [INFO] Task started: CheckM
[2024-01-24 12:39:55,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/checkm_input GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:40:19,510] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:19,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:19,534] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:19,534] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:19,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:40:19,535] [INFO] Task started: Blastn
[2024-01-24 12:40:19,535] [INFO] Running command: blastn -query GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga2a3ebd4-e3af-4a1f-9d55-59cf8be27c0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:20,596] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:20,600] [INFO] Selected 27 target genomes.
[2024-01-24 12:40:20,600] [INFO] Target genome list was writen to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:20,639] [INFO] Task started: fastANI
[2024-01-24 12:40:20,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eec3e62-ae5c-4693-b535-a6358cdc053b/GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna.gz --refList GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:34,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:34,277] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:34,277] [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
GCF_900112085.1	s__Acetitomaculum ruminis	100.0	994	999	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetitomaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900110975.1	s__CAG-603 sp900110975	77.4812	76	999	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-603	95.0	98.39	98.39	0.96	0.96	2	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	75.4277	55	999	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,279] [INFO] GTDB search result was written to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:34,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:34,282] [INFO] DFAST_QC result json was written to GCF_900112085.1_IMG-taxon_2651870361_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:40:34,282] [INFO] DFAST_QC completed!
[2024-01-24 12:40:34,282] [INFO] Total running time: 0h0m59s