[2024-01-24 12:30:52,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference
[2024-01-24 12:30:53,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,440] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,440] [INFO] Running command: gunzip -c /var/lib/cwl/stga2afee7e-c69f-465a-9efc-3ed6345c5bf3/GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/cds.fna -a GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:05,014] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:05,014] [INFO] Task started: HMMsearch
[2024-01-24 12:31:05,014] [INFO] Running command: hmmsearch --tblout GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/reference_markers.hmm GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:05,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:05,298] [INFO] Found 6/6 markers.
[2024-01-24 12:31:05,338] [INFO] Query marker FASTA was written to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:05,339] [INFO] Task started: Blastn
[2024-01-24 12:31:05,339] [INFO] Running command: blastn -query GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/reference_markers.fasta -out GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:06,051] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:06,056] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:06,057] [INFO] Target genome list was writen to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:06,066] [INFO] Task started: fastANI
[2024-01-24 12:31:06,066] [INFO] Running command: fastANI --query /var/lib/cwl/stga2afee7e-c69f-465a-9efc-3ed6345c5bf3/GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna.gz --refList GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:15,665] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:15,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:15,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:15,678] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:15,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:15,679] [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
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	100.0	1296	1297	95	conclusive
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	82.4687	813	1297	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	82.3976	832	1297	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	80.3353	629	1297	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	79.9796	650	1297	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.8927	602	1297	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	79.4717	554	1297	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	79.0555	480	1297	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.7674	254	1297	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.2842	272	1297	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.2384	234	1297	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.2265	233	1297	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.1431	230	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:15,681] [INFO] DFAST Taxonomy check result was written to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:15,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:15,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:15,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/checkm_data
[2024-01-24 12:31:15,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:15,723] [INFO] Task started: CheckM
[2024-01-24 12:31:15,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/checkm_input GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:52,706] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:52,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:52,725] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:52,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:52,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:52,727] [INFO] Task started: Blastn
[2024-01-24 12:31:52,727] [INFO] Running command: blastn -query GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e6e5c8a-0171-4911-82e7-5da2f177994b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:53,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:53,657] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:53,657] [INFO] Target genome list was writen to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:53,666] [INFO] Task started: fastANI
[2024-01-24 12:31:53,666] [INFO] Running command: fastANI --query /var/lib/cwl/stga2afee7e-c69f-465a-9efc-3ed6345c5bf3/GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna.gz --refList GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:03,565] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:03,583] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:03,584] [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_900188355.1	s__Lutibacter flavus	100.0	1295	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003384935.1	s__Lutibacter oceani	82.4709	813	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646675.1	s__Lutibacter litoralis	81.0007	682	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260195.1	s__Lutibacter citreus	80.3151	630	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	80.0232	658	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	79.9813	653	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	79.9141	600	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	79.8328	386	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	79.5689	512	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	79.4991	539	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106565.1	s__Lutibacter oricola	79.4679	554	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	79.3974	500	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015767395.1	s__Lutibacter sp015767395	79.3234	366	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:03,586] [INFO] GTDB search result was written to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:03,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:03,592] [INFO] DFAST_QC result json was written to GCF_900188355.1_IMG-taxon_2622736608_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:03,592] [INFO] DFAST_QC completed!
[2024-01-24 12:32:03,592] [INFO] Total running time: 0h1m12s