[2024-01-24 12:57:50,169] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference
[2024-01-24 12:57:51,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,313] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ab55d39-e50f-4273-96ac-f19614155be7/GCF_009901585.1_ASM990158v1_genomic.fna.gz | prodigal -d GCF_009901585.1_ASM990158v1_genomic.fna/cds.fna -a GCF_009901585.1_ASM990158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:12,809] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:12,809] [INFO] Task started: HMMsearch
[2024-01-24 12:58:12,810] [INFO] Running command: hmmsearch --tblout GCF_009901585.1_ASM990158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/reference_markers.hmm GCF_009901585.1_ASM990158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:13,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:13,053] [INFO] Found 6/6 markers.
[2024-01-24 12:58:13,093] [INFO] Query marker FASTA was written to GCF_009901585.1_ASM990158v1_genomic.fna/markers.fasta
[2024-01-24 12:58:13,093] [INFO] Task started: Blastn
[2024-01-24 12:58:13,093] [INFO] Running command: blastn -query GCF_009901585.1_ASM990158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/reference_markers.fasta -out GCF_009901585.1_ASM990158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:13,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:13,690] [INFO] Selected 24 target genomes.
[2024-01-24 12:58:13,690] [INFO] Target genome list was writen to GCF_009901585.1_ASM990158v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:13,699] [INFO] Task started: fastANI
[2024-01-24 12:58:13,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab55d39-e50f-4273-96ac-f19614155be7/GCF_009901585.1_ASM990158v1_genomic.fna.gz --refList GCF_009901585.1_ASM990158v1_genomic.fna/target_genomes.txt --output GCF_009901585.1_ASM990158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:29,453] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:29,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:29,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:29,469] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:29,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:29,470] [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
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	100.0	1654	1655	95	conclusive
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.9959	120	1655	95	below_threshold
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	76.952	119	1655	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.876	134	1655	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	76.7912	116	1655	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.6753	86	1655	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	76.6587	80	1655	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.4064	72	1655	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.4064	72	1655	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.3964	78	1655	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.3667	91	1655	95	below_threshold
Arenibacter certesii	strain=DSM 19833	GCA_000429545.1	228955	228955	type	True	76.2381	57	1655	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	76.218	82	1655	95	below_threshold
Arenibacter certesii	strain=KCTC 12113	GCA_014651295.1	228955	228955	type	True	76.2146	58	1655	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.2141	101	1655	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	76.1802	81	1655	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	76.092	57	1655	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.0378	56	1655	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.031	66	1655	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.0269	96	1655	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	75.872	54	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:29,471] [INFO] DFAST Taxonomy check result was written to GCF_009901585.1_ASM990158v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:29,472] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:29,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:29,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/checkm_data
[2024-01-24 12:58:29,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:29,517] [INFO] Task started: CheckM
[2024-01-24 12:58:29,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009901585.1_ASM990158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009901585.1_ASM990158v1_genomic.fna/checkm_input GCF_009901585.1_ASM990158v1_genomic.fna/checkm_result
[2024-01-24 12:59:29,808] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:29,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:29,829] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:29,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:29,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009901585.1_ASM990158v1_genomic.fna/markers.fasta)
[2024-01-24 12:59:29,829] [INFO] Task started: Blastn
[2024-01-24 12:59:29,829] [INFO] Running command: blastn -query GCF_009901585.1_ASM990158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f0e1188-1059-4fd9-a9e0-c0a9b2910022/dqc_reference/reference_markers_gtdb.fasta -out GCF_009901585.1_ASM990158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:59:30,644] [INFO] Task succeeded: Blastn
[2024-01-24 12:59:30,648] [INFO] Selected 24 target genomes.
[2024-01-24 12:59:30,648] [INFO] Target genome list was writen to GCF_009901585.1_ASM990158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:59:30,838] [INFO] Task started: fastANI
[2024-01-24 12:59:30,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ab55d39-e50f-4273-96ac-f19614155be7/GCF_009901585.1_ASM990158v1_genomic.fna.gz --refList GCF_009901585.1_ASM990158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009901585.1_ASM990158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:45,736] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:45,755] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:45,755] [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
GCA_009901585.1	s__R33 sp009901585	100.0	1654	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__R33	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013042925.1	s__Eudoraea sp013042925	77.0601	71	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	98.51	98.47	0.72	0.70	3	-
GCF_014638095.1	s__Muriicola marianensis	76.979	120	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.8737	133	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042125.1	s__Muriicola sp013042125	76.8063	75	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004139715.1	s__Muriicola sp004139715	76.7912	116	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.7121	130	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.7016	85	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909255.1	s__Arenibacter hampyeongensis	76.6587	80	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041785.1	s__Eudoraea sp013041785	76.5344	85	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	97.28	95.79	0.83	0.71	4	-
GCF_011927795.1	s__Saonia flava	76.5315	88	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	76.4667	83	1655	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_017313275.1	s__Muricauda lutimaris_A	76.4448	76	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	76.4342	71	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.4074	89	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	76.4053	69	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429545.1	s__Arenibacter certesii	76.266	56	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.98	99.98	0.99	0.99	2	-
GCF_009184425.1	s__Muricauda olearia	76.2476	99	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_000733925.1	s__Arenibacter algicola	76.2149	97	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_900103215.1	s__Kriegella aquimaris	76.2112	81	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957295.1	s__Arenibacter aquaticus	76.1685	80	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.154	79	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.1337	88	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003259375.1	s__Arenibacter echinorum	76.0424	96	1655	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:59:45,757] [INFO] GTDB search result was written to GCF_009901585.1_ASM990158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:45,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:45,764] [INFO] DFAST_QC result json was written to GCF_009901585.1_ASM990158v1_genomic.fna/dqc_result.json
[2024-01-24 12:59:45,764] [INFO] DFAST_QC completed!
[2024-01-24 12:59:45,764] [INFO] Total running time: 0h1m56s