[2024-01-24 15:18:38,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference
[2024-01-24 15:18:39,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,515] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,516] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb73add-800e-4aa4-bcdd-6879e4c9ae39/GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/cds.fna -a GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:01,302] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:01,302] [INFO] Task started: HMMsearch
[2024-01-24 15:19:01,302] [INFO] Running command: hmmsearch --tblout GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/reference_markers.hmm GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:01,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:01,682] [INFO] Found 6/6 markers.
[2024-01-24 15:19:01,724] [INFO] Query marker FASTA was written to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:19:01,724] [INFO] Task started: Blastn
[2024-01-24 15:19:01,724] [INFO] Running command: blastn -query GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/reference_markers.fasta -out GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:02,341] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:02,345] [INFO] Selected 23 target genomes.
[2024-01-24 15:19:02,346] [INFO] Target genome list was writen to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:19:02,363] [INFO] Task started: fastANI
[2024-01-24 15:19:02,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb73add-800e-4aa4-bcdd-6879e4c9ae39/GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna.gz --refList GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:26,566] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:26,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:26,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:26,583] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:26,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:26,583] [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
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	100.0	1534	1534	95	conclusive
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	77.0629	51	1534	95	below_threshold
Flavisolibacter ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	76.8659	85	1534	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.7592	117	1534	95	below_threshold
Flavisolibacter tropicus	strain=LCS9	GCA_001644645.1	1492898	1492898	type	True	76.7142	142	1534	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.652	61	1534	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.5684	53	1534	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.3244	51	1534	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.2953	52	1534	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.2864	64	1534	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.2846	58	1534	95	below_threshold
Flavihumibacter solisilvae	strain=3-3	GCA_000814475.1	1349421	1349421	type	True	76.2773	61	1534	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.2463	53	1534	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0879	62	1534	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.0733	64	1534	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.0381	64	1534	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.8034	63	1534	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.7526	62	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:26,585] [INFO] DFAST Taxonomy check result was written to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:19:26,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:26,587] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:26,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/checkm_data
[2024-01-24 15:19:26,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:26,636] [INFO] Task started: CheckM
[2024-01-24 15:19:26,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/checkm_input GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:20:26,021] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:26,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:26,043] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:26,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:26,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:20:26,045] [INFO] Task started: Blastn
[2024-01-24 15:20:26,045] [INFO] Running command: blastn -query GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c7cc8c8-5de3-4773-b450-a8abdd34117e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:26,825] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:26,838] [INFO] Selected 22 target genomes.
[2024-01-24 15:20:26,838] [INFO] Target genome list was writen to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:26,872] [INFO] Task started: fastANI
[2024-01-24 15:20:26,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb73add-800e-4aa4-bcdd-6879e4c9ae39/GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna.gz --refList GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:43,793] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:43,812] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:43,813] [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_900129295.1	s__Flavisolibacter ginsengisoli	100.0	1534	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017745135.1	s__Flavisolibacter sp017745135	76.9209	110	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.8637	114	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644645.1	s__Flavisolibacter_B tropicus	76.8035	143	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.7788	116	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830055.1	s__Lacibacter cauensis	76.6521	61	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	76.4961	54	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185185.1	s__AWTP1-9 sp016185185	76.4526	57	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720585.1	s__JJ008 sp016720585	76.4297	59	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.96	98.85	0.95	0.92	4	-
GCA_002050435.1	s__Flavisolibacter sp002050435	76.4245	149	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708765.1	s__JJ008 sp016708765	76.3645	60	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.32	99.14	0.92	0.90	6	-
GCF_015831355.1	s__Panacibacter sp015831355	76.3244	51	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721085.1	s__UBA3961 sp016721085	76.2878	59	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA3961	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814475.1	s__Flavihumibacter solisilvae	76.27	60	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014168535.1	s__Lacibacter sp014168535	76.2359	65	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	76.1057	92	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267535.1	s__JAFDYH01 sp018267535	75.9479	69	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFDYH01	95.0	98.33	98.33	0.81	0.81	2	-
GCF_900110245.1	s__Niastella yeongjuensis	75.7526	62	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016787085.1	s__VBAT01 sp016787085	75.4918	81	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266775.1	s__Ferruginibacter sp018266775	75.4348	78	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:43,815] [INFO] GTDB search result was written to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:43,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:43,820] [INFO] DFAST_QC result json was written to GCF_900129295.1_IMG-taxon_2582580745_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:20:43,820] [INFO] DFAST_QC completed!
[2024-01-24 15:20:43,820] [INFO] Total running time: 0h2m6s