[2024-01-24 13:25:31,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,352] [INFO] DQC Reference Directory: /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference
[2024-01-24 13:25:32,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,693] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg4621d6d3-a9d6-40c9-9507-07ce2c04ba7f/GCF_004378585.1_ASM437858v1_genomic.fna.gz | prodigal -d GCF_004378585.1_ASM437858v1_genomic.fna/cds.fna -a GCF_004378585.1_ASM437858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:43,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:43,306] [INFO] Task started: HMMsearch
[2024-01-24 13:25:43,306] [INFO] Running command: hmmsearch --tblout GCF_004378585.1_ASM437858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/reference_markers.hmm GCF_004378585.1_ASM437858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:43,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:43,605] [INFO] Found 6/6 markers.
[2024-01-24 13:25:43,635] [INFO] Query marker FASTA was written to GCF_004378585.1_ASM437858v1_genomic.fna/markers.fasta
[2024-01-24 13:25:43,636] [INFO] Task started: Blastn
[2024-01-24 13:25:43,636] [INFO] Running command: blastn -query GCF_004378585.1_ASM437858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/reference_markers.fasta -out GCF_004378585.1_ASM437858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:44,342] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:44,346] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:44,347] [INFO] Target genome list was writen to GCF_004378585.1_ASM437858v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:44,352] [INFO] Task started: fastANI
[2024-01-24 13:25:44,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg4621d6d3-a9d6-40c9-9507-07ce2c04ba7f/GCF_004378585.1_ASM437858v1_genomic.fna.gz --refList GCF_004378585.1_ASM437858v1_genomic.fna/target_genomes.txt --output GCF_004378585.1_ASM437858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:52,937] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:52,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:52,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:52,955] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:52,955] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:25:52,956] [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 oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	81.8325	725	1198	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	81.718	741	1198	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	81.0552	679	1198	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	80.1446	608	1198	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	80.0069	629	1198	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.9986	575	1198	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	78.6301	467	1198	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.2814	241	1198	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.2007	279	1198	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.1099	237	1198	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.8363	240	1198	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	76.8094	204	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:52,957] [INFO] DFAST Taxonomy check result was written to GCF_004378585.1_ASM437858v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:52,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:52,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:52,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/checkm_data
[2024-01-24 13:25:52,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:52,999] [INFO] Task started: CheckM
[2024-01-24 13:25:52,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004378585.1_ASM437858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004378585.1_ASM437858v1_genomic.fna/checkm_input GCF_004378585.1_ASM437858v1_genomic.fna/checkm_result
[2024-01-24 13:26:27,483] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:27,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:27,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:27,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:27,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004378585.1_ASM437858v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:27,507] [INFO] Task started: Blastn
[2024-01-24 13:26:27,507] [INFO] Running command: blastn -query GCF_004378585.1_ASM437858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged816f94-5781-4955-828a-a54f9eb16e60/dqc_reference/reference_markers_gtdb.fasta -out GCF_004378585.1_ASM437858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:28,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:28,410] [INFO] Selected 14 target genomes.
[2024-01-24 13:26:28,410] [INFO] Target genome list was writen to GCF_004378585.1_ASM437858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:28,444] [INFO] Task started: fastANI
[2024-01-24 13:26:28,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg4621d6d3-a9d6-40c9-9507-07ce2c04ba7f/GCF_004378585.1_ASM437858v1_genomic.fna.gz --refList GCF_004378585.1_ASM437858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004378585.1_ASM437858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:38,772] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:38,796] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:38,796] [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_014646675.1	s__Lutibacter litoralis	99.9958	1178	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003384935.1	s__Lutibacter oceani	81.8559	722	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188355.1	s__Lutibacter flavus	81.0293	681	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	80.1575	606	1198	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	80.0363	568	1198	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	80.0001	631	1198	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	79.8979	614	1198	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	79.716	340	1198	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	79.3663	459	1198	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	79.3579	511	1198	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	79.1196	463	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012524075.1	s__Lutibacter sp012524075	78.9639	488	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	78.9048	376	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	78.6294	466	1198	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 13:26:38,799] [INFO] GTDB search result was written to GCF_004378585.1_ASM437858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:38,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:38,803] [INFO] DFAST_QC result json was written to GCF_004378585.1_ASM437858v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:38,803] [INFO] DFAST_QC completed!
[2024-01-24 13:26:38,803] [INFO] Total running time: 0h1m7s