[2023-03-16 07:55:45,172] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,172] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,172] [INFO] DQC Reference Directory: /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stge297bd05-3220-4d34-8e44-fb1e7d2d08f4/OceanDNA-b6259.fa | prodigal -d OceanDNA-b6259/cds.fna -a OceanDNA-b6259/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:17,014] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:17,015] [INFO] Task started: HMMsearch
[2023-03-16 07:56:17,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b6259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/reference_markers.hmm OceanDNA-b6259/protein.faa > /dev/null
[2023-03-16 07:56:17,216] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:17,216] [INFO] Found 6/6 markers.
[2023-03-16 07:56:17,236] [INFO] Query marker FASTA was written to OceanDNA-b6259/markers.fasta
[2023-03-16 07:56:17,237] [INFO] Task started: Blastn
[2023-03-16 07:56:17,237] [INFO] Running command: blastn -query OceanDNA-b6259/markers.fasta -db /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/reference_markers.fasta -out OceanDNA-b6259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:17,794] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:17,795] [INFO] Selected 29 target genomes.
[2023-03-16 07:56:17,795] [INFO] Target genome list was writen to OceanDNA-b6259/target_genomes.txt
[2023-03-16 07:56:17,812] [INFO] Task started: fastANI
[2023-03-16 07:56:17,827] [INFO] Running command: fastANI --query /var/lib/cwl/stge297bd05-3220-4d34-8e44-fb1e7d2d08f4/OceanDNA-b6259.fa --refList OceanDNA-b6259/target_genomes.txt --output OceanDNA-b6259/fastani_result.tsv --threads 1
[2023-03-16 07:56:35,471] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:35,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:35,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:35,487] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:35,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:35,487] [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
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	77.067	147	1158	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	76.8922	143	1158	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.8807	132	1158	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.8753	131	1158	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.8262	109	1158	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.8173	143	1158	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.799	115	1158	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.7217	126	1158	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.7099	137	1158	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.694	138	1158	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.6903	160	1158	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.6634	118	1158	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	76.6529	153	1158	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.5288	108	1158	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.5285	108	1158	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	76.4687	146	1158	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	76.2647	63	1158	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	76.237	64	1158	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.1427	81	1158	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.1427	81	1158	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.0409	87	1158	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	76.0329	68	1158	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	75.9992	67	1158	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	75.9687	71	1158	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	75.9117	87	1158	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	75.7717	76	1158	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	75.7499	74	1158	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	75.6979	62	1158	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:35,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6259/tc_result.tsv
[2023-03-16 07:56:35,490] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:35,490] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:35,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/checkm_data
[2023-03-16 07:56:35,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:35,499] [INFO] Task started: CheckM
[2023-03-16 07:56:35,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6259/checkm_input OceanDNA-b6259/checkm_result
[2023-03-16 07:57:51,601] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:51,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:51,623] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:51,623] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:51,623] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6259/markers.fasta)
[2023-03-16 07:57:51,624] [INFO] Task started: Blastn
[2023-03-16 07:57:51,624] [INFO] Running command: blastn -query OceanDNA-b6259/markers.fasta -db /var/lib/cwl/stg624570ad-2a7b-496c-aff5-7638da53abc1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:52,384] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:52,385] [INFO] Selected 26 target genomes.
[2023-03-16 07:57:52,385] [INFO] Target genome list was writen to OceanDNA-b6259/target_genomes_gtdb.txt
[2023-03-16 07:57:52,886] [INFO] Task started: fastANI
[2023-03-16 07:57:52,886] [INFO] Running command: fastANI --query /var/lib/cwl/stge297bd05-3220-4d34-8e44-fb1e7d2d08f4/OceanDNA-b6259.fa --refList OceanDNA-b6259/target_genomes_gtdb.txt --output OceanDNA-b6259/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:58:09,026] [INFO] Task succeeded: fastANI
[2023-03-16 07:58:09,039] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:58:09,040] [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_013214065.1	s__DT-32 sp013214065	99.956	1116	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003584105.1	s__Muricauda taeanensis	76.895	142	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_013090115.1	s__Muricauda amphidinii	76.8713	107	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	76.8338	142	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	76.8262	85	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	76.8204	114	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.8096	140	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCA_009797885.1	s__Croceivirga sp009797885	76.7674	147	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.6903	160	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	76.6701	107	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	76.6616	117	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963865.1	s__Muricauda_A lutaonensis	76.6529	153	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	97.74	97.69	0.86	0.85	5	-
GCF_002742265.1	s__Maribacter sp002742265	76.5852	70	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.5689	94	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.5288	108	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017795065.1	s__Muricauda sp017795065	76.498	106	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009903685.1	s__Muricauda ochracea	76.4958	100	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	76.4687	146	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	76.405	135	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	76.2647	63	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003232435.1	s__Aurantibacter_A sp003232435	76.1729	54	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.1427	81	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_013402795.1	s__Costertonia aggregata	75.9297	86	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Costertonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	75.7717	76	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_003933245.1	s__Maribacter algicola	75.6979	62	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:58:09,041] [INFO] GTDB search result was written to OceanDNA-b6259/result_gtdb.tsv
[2023-03-16 07:58:09,047] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:58:09,050] [INFO] DFAST_QC result json was written to OceanDNA-b6259/dqc_result.json
[2023-03-16 07:58:09,050] [INFO] DFAST_QC completed!
[2023-03-16 07:58:09,050] [INFO] Total running time: 0h2m24s