[2023-03-15 13:00:04,932] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:00:04,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:00:04,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference
[2023-03-15 13:00:06,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:00:06,091] [INFO] Task started: Prodigal
[2023-03-15 13:00:06,091] [INFO] Running command: cat /var/lib/cwl/stg125c0ac0-089c-4a3c-b23a-ddd6489e6ee4/OceanDNA-b10052.fa | prodigal -d OceanDNA-b10052/cds.fna -a OceanDNA-b10052/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:00:28,070] [INFO] Task succeeded: Prodigal
[2023-03-15 13:00:28,071] [INFO] Task started: HMMsearch
[2023-03-15 13:00:28,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b10052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/reference_markers.hmm OceanDNA-b10052/protein.faa > /dev/null
[2023-03-15 13:00:28,264] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:00:28,264] [INFO] Found 6/6 markers.
[2023-03-15 13:00:28,282] [INFO] Query marker FASTA was written to OceanDNA-b10052/markers.fasta
[2023-03-15 13:00:28,282] [INFO] Task started: Blastn
[2023-03-15 13:00:28,282] [INFO] Running command: blastn -query OceanDNA-b10052/markers.fasta -db /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/reference_markers.fasta -out OceanDNA-b10052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:00:28,855] [INFO] Task succeeded: Blastn
[2023-03-15 13:00:28,855] [INFO] Selected 30 target genomes.
[2023-03-15 13:00:28,856] [INFO] Target genome list was writen to OceanDNA-b10052/target_genomes.txt
[2023-03-15 13:00:28,872] [INFO] Task started: fastANI
[2023-03-15 13:00:28,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg125c0ac0-089c-4a3c-b23a-ddd6489e6ee4/OceanDNA-b10052.fa --refList OceanDNA-b10052/target_genomes.txt --output OceanDNA-b10052/fastani_result.tsv --threads 1
[2023-03-15 13:00:44,472] [INFO] Task succeeded: fastANI
[2023-03-15 13:00:44,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:00:44,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:00:44,487] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:00:44,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:00:44,488] [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
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	77.3131	90	984	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.1541	140	984	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	77.055	104	984	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	77.0169	104	984	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.9927	107	984	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.963	144	984	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.9171	141	984	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.9056	121	984	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.8986	125	984	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.8812	142	984	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.811	110	984	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.7731	111	984	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.7197	152	984	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	76.713	135	984	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.6987	123	984	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.6961	143	984	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.6816	141	984	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.5971	131	984	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	76.5627	150	984	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.5621	152	984	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.5139	112	984	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.4927	117	984	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.4674	140	984	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	76.4448	105	984	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.1924	134	984	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.1886	137	984	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	76.0938	68	984	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:00:44,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10052/tc_result.tsv
[2023-03-15 13:00:44,488] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:00:44,488] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:00:44,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/checkm_data
[2023-03-15 13:00:44,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:00:44,523] [INFO] Task started: CheckM
[2023-03-15 13:00:44,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10052/checkm_input OceanDNA-b10052/checkm_result
[2023-03-15 13:01:41,299] [INFO] Task succeeded: CheckM
[2023-03-15 13:01:41,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:01:41,325] [INFO] ===== Completeness check finished =====
[2023-03-15 13:01:41,325] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:01:41,325] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10052/markers.fasta)
[2023-03-15 13:01:41,327] [INFO] Task started: Blastn
[2023-03-15 13:01:41,327] [INFO] Running command: blastn -query OceanDNA-b10052/markers.fasta -db /var/lib/cwl/stgd0787f45-195c-440d-a9d1-c6cc5f6d27a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:01:42,126] [INFO] Task succeeded: Blastn
[2023-03-15 13:01:42,128] [INFO] Selected 22 target genomes.
[2023-03-15 13:01:42,128] [INFO] Target genome list was writen to OceanDNA-b10052/target_genomes_gtdb.txt
[2023-03-15 13:01:42,300] [INFO] Task started: fastANI
[2023-03-15 13:01:42,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg125c0ac0-089c-4a3c-b23a-ddd6489e6ee4/OceanDNA-b10052.fa --refList OceanDNA-b10052/target_genomes_gtdb.txt --output OceanDNA-b10052/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:01:56,356] [INFO] Task succeeded: fastANI
[2023-03-15 13:01:56,368] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:01:56,368] [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_002471825.1	s__Polaribacter sp002471825	99.995	967	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003129485.1	s__Polaribacter sp003129485	77.1541	140	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867075.1	s__Tenacibaculum mesophilum	77.0179	105	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_003335085.1	s__Polaribacter sp003335085	77.0079	118	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.8812	142	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016858305.2	s__Polaribacter sp016858305	76.8659	107	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.7941	110	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	76.7195	152	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767435.1	s__Polaribacter sp015767435	76.703	155	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	76.6987	123	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_014784055.1	s__Polaribacter haliotis	76.6961	143	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373105.1	s__Polaribacter sp013373105	76.6333	133	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	76.5773	151	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.5487	129	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.5331	111	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.5093	116	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	76.4775	140	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	76.4516	139	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387615.1	s__Tenacibaculum gallaicum	76.4448	105	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	76.3861	114	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214275.1	s__SCGC-AAA160-P02 sp013214275	76.2652	50	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	76.1184	67	984	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:01:56,369] [INFO] GTDB search result was written to OceanDNA-b10052/result_gtdb.tsv
[2023-03-15 13:01:56,370] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:01:56,373] [INFO] DFAST_QC result json was written to OceanDNA-b10052/dqc_result.json
[2023-03-15 13:01:56,373] [INFO] DFAST_QC completed!
[2023-03-15 13:01:56,373] [INFO] Total running time: 0h1m51s