[2024-01-25 20:23:35,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:35,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:35,598] [INFO] DQC Reference Directory: /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference
[2024-01-25 20:23:36,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:36,767] [INFO] Task started: Prodigal
[2024-01-25 20:23:36,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d1f5a4-0bc4-4c13-88e3-62e7630cc6d1/GCF_014596745.1_ASM1459674v1_genomic.fna.gz | prodigal -d GCF_014596745.1_ASM1459674v1_genomic.fna/cds.fna -a GCF_014596745.1_ASM1459674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:56,491] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:56,492] [INFO] Task started: HMMsearch
[2024-01-25 20:23:56,492] [INFO] Running command: hmmsearch --tblout GCF_014596745.1_ASM1459674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/reference_markers.hmm GCF_014596745.1_ASM1459674v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:56,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:56,746] [INFO] Found 6/6 markers.
[2024-01-25 20:23:56,788] [INFO] Query marker FASTA was written to GCF_014596745.1_ASM1459674v1_genomic.fna/markers.fasta
[2024-01-25 20:23:56,788] [INFO] Task started: Blastn
[2024-01-25 20:23:56,788] [INFO] Running command: blastn -query GCF_014596745.1_ASM1459674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/reference_markers.fasta -out GCF_014596745.1_ASM1459674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:57,407] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:57,411] [INFO] Selected 13 target genomes.
[2024-01-25 20:23:57,411] [INFO] Target genome list was writen to GCF_014596745.1_ASM1459674v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:57,422] [INFO] Task started: fastANI
[2024-01-25 20:23:57,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d1f5a4-0bc4-4c13-88e3-62e7630cc6d1/GCF_014596745.1_ASM1459674v1_genomic.fna.gz --refList GCF_014596745.1_ASM1459674v1_genomic.fna/target_genomes.txt --output GCF_014596745.1_ASM1459674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:08,541] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:08,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:08,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:08,551] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:24:08,551] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:24:08,551] [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
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	92.7826	1305	1608	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	92.7704	1315	1608	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	81.2154	892	1608	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	78.7287	575	1608	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	77.304	163	1608	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	77.0548	208	1608	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	77.003	190	1608	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.7936	150	1608	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.7401	189	1608	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	76.5867	171	1608	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	76.5259	146	1608	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	76.1862	88	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:08,552] [INFO] DFAST Taxonomy check result was written to GCF_014596745.1_ASM1459674v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:08,553] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:08,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:08,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/checkm_data
[2024-01-25 20:24:08,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:08,600] [INFO] Task started: CheckM
[2024-01-25 20:24:08,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596745.1_ASM1459674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596745.1_ASM1459674v1_genomic.fna/checkm_input GCF_014596745.1_ASM1459674v1_genomic.fna/checkm_result
[2024-01-25 20:25:03,302] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:03,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:03,329] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:03,330] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:03,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596745.1_ASM1459674v1_genomic.fna/markers.fasta)
[2024-01-25 20:25:03,330] [INFO] Task started: Blastn
[2024-01-25 20:25:03,330] [INFO] Running command: blastn -query GCF_014596745.1_ASM1459674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge96ca588-a414-4ff7-984e-ce8b449f763c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596745.1_ASM1459674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:04,223] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:04,225] [INFO] Selected 10 target genomes.
[2024-01-25 20:25:04,226] [INFO] Target genome list was writen to GCF_014596745.1_ASM1459674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:04,243] [INFO] Task started: fastANI
[2024-01-25 20:25:04,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d1f5a4-0bc4-4c13-88e3-62e7630cc6d1/GCF_014596745.1_ASM1459674v1_genomic.fna.gz --refList GCF_014596745.1_ASM1459674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596745.1_ASM1459674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:12,580] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:12,587] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:12,588] [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_014596745.1	s__Maribacter_A sp014596745	100.0	1605	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148665.1	s__Maribacter_A polysiphoniae	92.7816	1314	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCA_002749285.1	s__Maribacter_A sp002749285	83.093	531	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	81.1974	895	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014610845.1	s__Maribacter_A arenosus	78.7362	574	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	77.9817	344	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018679695.1	s__Maribacter_A sp018679695	77.598	309	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.00	99.00	0.82	0.82	2	-
GCF_005885635.1	s__RZ26 sp005885635	76.7936	150	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.4094	53	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963865.1	s__Muricauda_A lutaonensis	76.1862	88	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	97.74	97.69	0.86	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:12,589] [INFO] GTDB search result was written to GCF_014596745.1_ASM1459674v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:12,589] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:12,592] [INFO] DFAST_QC result json was written to GCF_014596745.1_ASM1459674v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:12,592] [INFO] DFAST_QC completed!
[2024-01-25 20:25:12,592] [INFO] Total running time: 0h1m37s