[2024-01-24 12:37:22,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:22,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:22,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference
[2024-01-24 12:37:23,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:23,716] [INFO] Task started: Prodigal
[2024-01-24 12:37:23,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3af03dc-4b15-4539-bbaf-464403da7fbc/GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/cds.fna -a GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:37,616] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:37,617] [INFO] Task started: HMMsearch
[2024-01-24 12:37:37,617] [INFO] Running command: hmmsearch --tblout GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/reference_markers.hmm GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:37,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:37,936] [INFO] Found 6/6 markers.
[2024-01-24 12:37:37,978] [INFO] Query marker FASTA was written to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:37:37,978] [INFO] Task started: Blastn
[2024-01-24 12:37:37,978] [INFO] Running command: blastn -query GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/reference_markers.fasta -out GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:38,624] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:38,627] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:38,627] [INFO] Target genome list was writen to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:37:38,633] [INFO] Task started: fastANI
[2024-01-24 12:37:38,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3af03dc-4b15-4539-bbaf-464403da7fbc/GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna.gz --refList GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:48,664] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:48,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:48,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:48,683] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:48,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:48,683] [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
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	100.0	1400	1403	95	conclusive
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	88.5202	1043	1403	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	88.4519	1026	1403	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	88.0158	1003	1403	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	87.9286	1019	1403	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	85.9537	834	1403	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	85.9155	964	1403	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	85.8411	846	1403	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	84.2503	835	1403	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.7949	74	1403	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.44	104	1403	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	75.7732	64	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:48,685] [INFO] DFAST Taxonomy check result was written to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:37:48,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:48,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:48,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/checkm_data
[2024-01-24 12:37:48,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:48,730] [INFO] Task started: CheckM
[2024-01-24 12:37:48,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/checkm_input GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:38:30,864] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:30,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:30,884] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:30,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:30,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:38:30,885] [INFO] Task started: Blastn
[2024-01-24 12:38:30,885] [INFO] Running command: blastn -query GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e4e9dbb-bead-4fe8-9dd3-c8685c09a924/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:31,739] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:31,741] [INFO] Selected 8 target genomes.
[2024-01-24 12:38:31,742] [INFO] Target genome list was writen to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:31,747] [INFO] Task started: fastANI
[2024-01-24 12:38:31,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3af03dc-4b15-4539-bbaf-464403da7fbc/GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna.gz --refList GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:39,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:39,241] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:39,242] [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_900113135.1	s__Salegentibacter agarivorans	100.0	1400	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	conclusive
GCF_900168115.1	s__Salegentibacter salinarum	88.5089	1044	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142975.1	s__Salegentibacter salegens	87.9197	1022	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168265.1	s__Salegentibacter salarius	85.9488	834	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_002900095.1	s__Salegentibacter mishustinae	85.6084	903	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.4384	940	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	83.9698	817	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	76.3077	76	1403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:39,244] [INFO] GTDB search result was written to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:39,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:39,248] [INFO] DFAST_QC result json was written to GCF_900113135.1_IMG-taxon_2622736526_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:38:39,248] [INFO] DFAST_QC completed!
[2024-01-24 12:38:39,249] [INFO] Total running time: 0h1m17s