[2024-01-24 12:47:12,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference
[2024-01-24 12:47:13,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,612] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,612] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8507f12-c8bc-454d-b311-0638c7979089/GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/cds.fna -a GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:43,178] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:43,179] [INFO] Task started: HMMsearch
[2024-01-24 12:47:43,179] [INFO] Running command: hmmsearch --tblout GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/reference_markers.hmm GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:43,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:43,498] [INFO] Found 6/6 markers.
[2024-01-24 12:47:43,554] [INFO] Query marker FASTA was written to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:43,554] [INFO] Task started: Blastn
[2024-01-24 12:47:43,554] [INFO] Running command: blastn -query GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/reference_markers.fasta -out GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:44,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:44,174] [INFO] Selected 26 target genomes.
[2024-01-24 12:47:44,175] [INFO] Target genome list was writen to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:44,190] [INFO] Task started: fastANI
[2024-01-24 12:47:44,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8507f12-c8bc-454d-b311-0638c7979089/GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna.gz --refList GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:09,138] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:09,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:09,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:09,148] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:09,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:09,148] [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
Siphonobacter aquaeclarae	strain=DSM 21668	GCA_900103285.1	563176	563176	type	True	100.0	2053	2054	95	conclusive
Siphonobacter curvatus	strain=HR-U	GCA_002943425.1	2094562	2094562	type	True	77.0259	315	2054	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	76.0131	67	2054	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	75.7754	106	2054	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	75.7537	89	2054	95	below_threshold
Telluribacter humicola	strain=KCTC 42819	GCA_017355935.1	1720261	1720261	type	True	75.7068	54	2054	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.674	94	2054	95	below_threshold
Arsenicibacter rosenii	strain=SM-1	GCA_001870735.1	1750698	1750698	type	True	75.6202	93	2054	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	75.6194	82	2054	95	below_threshold
Rhabdobacter roseus	strain=DSM 105074	GCA_014202275.1	1655419	1655419	type	True	75.5361	79	2054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:09,150] [INFO] DFAST Taxonomy check result was written to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:48:09,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:09,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:09,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/checkm_data
[2024-01-24 12:48:09,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:09,208] [INFO] Task started: CheckM
[2024-01-24 12:48:09,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/checkm_input GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:49:28,772] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:28,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:28,800] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:28,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:28,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:49:28,801] [INFO] Task started: Blastn
[2024-01-24 12:49:28,801] [INFO] Running command: blastn -query GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg250929d9-004c-417e-8c90-918a16f427fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:29,596] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:29,601] [INFO] Selected 27 target genomes.
[2024-01-24 12:49:29,601] [INFO] Target genome list was writen to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:29,651] [INFO] Task started: fastANI
[2024-01-24 12:49:29,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8507f12-c8bc-454d-b311-0638c7979089/GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna.gz --refList GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:53,678] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:53,692] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:53,693] [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_900103285.1	s__Siphonobacter aquaeclarae	100.0	2053	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002838835.1	s__Siphonobacter sp002838835	77.1755	195	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872335.1	s__Siphonobacter sp002872335	77.0371	309	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	98.05	98.05	0.92	0.92	2	-
GCF_002943425.1	s__Siphonobacter curvatus	77.0259	315	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366505.1	s__Larkinella sp004366505	76.1126	95	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	76.0131	67	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	75.8615	70	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002825.1	s__Spirosoma oryzae	75.7537	89	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355935.1	s__Telluribacter humicola	75.7068	54	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Telluribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	75.6995	94	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202275.1	s__Rhabdobacter roseus	75.5361	79	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rhabdobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353175.1	s__Fibrella sp017353175	75.353	62	2054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:53,694] [INFO] GTDB search result was written to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:53,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:53,698] [INFO] DFAST_QC result json was written to GCF_900103285.1_IMG-taxon_2622736636_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:49:53,699] [INFO] DFAST_QC completed!
[2024-01-24 12:49:53,699] [INFO] Total running time: 0h2m41s