[2023-03-17 11:08:00,269] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,270] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,270] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference
[2023-03-17 11:08:01,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,420] [INFO] Running command: cat /var/lib/cwl/stg53df8acb-303f-4746-8617-4cd36ef7f668/OceanDNA-b10305.fa | prodigal -d OceanDNA-b10305/cds.fna -a OceanDNA-b10305/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:14,153] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:14,153] [INFO] Task started: HMMsearch
[2023-03-17 11:08:14,154] [INFO] Running command: hmmsearch --tblout OceanDNA-b10305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/reference_markers.hmm OceanDNA-b10305/protein.faa > /dev/null
[2023-03-17 11:08:14,364] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:14,364] [INFO] Found 6/6 markers.
[2023-03-17 11:08:14,417] [INFO] Query marker FASTA was written to OceanDNA-b10305/markers.fasta
[2023-03-17 11:08:14,418] [INFO] Task started: Blastn
[2023-03-17 11:08:14,418] [INFO] Running command: blastn -query OceanDNA-b10305/markers.fasta -db /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/reference_markers.fasta -out OceanDNA-b10305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:15,021] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:15,027] [INFO] Selected 25 target genomes.
[2023-03-17 11:08:15,027] [INFO] Target genome list was writen to OceanDNA-b10305/target_genomes.txt
[2023-03-17 11:08:15,040] [INFO] Task started: fastANI
[2023-03-17 11:08:15,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg53df8acb-303f-4746-8617-4cd36ef7f668/OceanDNA-b10305.fa --refList OceanDNA-b10305/target_genomes.txt --output OceanDNA-b10305/fastani_result.tsv --threads 1
[2023-03-17 11:08:28,615] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:28,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:28,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:28,630] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:28,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:28,631] [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
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.7685	267	692	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.693	234	692	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.669	259	692	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.6093	263	692	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.5941	241	692	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	77.5881	240	692	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	77.5634	254	692	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.5177	242	692	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.5063	251	692	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.4947	244	692	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.4468	250	692	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.4157	240	692	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	77.3257	241	692	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.3169	241	692	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.3136	251	692	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	77.3066	273	692	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	77.303	175	692	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.2984	257	692	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	77.2951	275	692	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.2915	250	692	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.2716	257	692	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.2685	254	692	95	below_threshold
Tenacibaculum maritimum		GCA_900119795.1	107401	107401	type	True	76.8812	156	692	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	76.6566	155	692	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	76.4796	139	692	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:28,633] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10305/tc_result.tsv
[2023-03-17 11:08:28,638] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:28,638] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:28,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/checkm_data
[2023-03-17 11:08:28,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:28,648] [INFO] Task started: CheckM
[2023-03-17 11:08:28,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10305/checkm_input OceanDNA-b10305/checkm_result
[2023-03-17 11:09:03,906] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:03,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:04,020] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:04,020] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:04,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10305/markers.fasta)
[2023-03-17 11:09:04,020] [INFO] Task started: Blastn
[2023-03-17 11:09:04,021] [INFO] Running command: blastn -query OceanDNA-b10305/markers.fasta -db /var/lib/cwl/stgf4ca456d-516f-465c-803b-055d6c5b93b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:04,869] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:04,874] [INFO] Selected 20 target genomes.
[2023-03-17 11:09:04,875] [INFO] Target genome list was writen to OceanDNA-b10305/target_genomes_gtdb.txt
[2023-03-17 11:09:05,073] [INFO] Task started: fastANI
[2023-03-17 11:09:05,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg53df8acb-303f-4746-8617-4cd36ef7f668/OceanDNA-b10305.fa --refList OceanDNA-b10305/target_genomes_gtdb.txt --output OceanDNA-b10305/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:16,354] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:16,366] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:09:16,366] [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_000383355.1	s__SCGC-AAA160-P02 sp000383355	98.3267	597	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	conclusive
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	82.3081	348	692	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	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	81.807	501	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	81.135	371	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCF_002163835.1	s__Polaribacter sp002163835	77.9324	282	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	77.8957	261	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	77.8574	298	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	77.7681	267	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	77.6729	256	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	77.6449	261	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900106075.1	s__Polaribacter sp900106075	77.5969	255	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_002954605.1	s__Polaribacter butkevichii	77.5634	254	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	77.5478	222	692	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	77.5436	240	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	77.4974	251	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	77.4971	247	692	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	77.2984	257	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335085.1	s__Polaribacter sp003335085	77.27	222	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	76.4796	139	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.2914	139	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:16,369] [INFO] GTDB search result was written to OceanDNA-b10305/result_gtdb.tsv
[2023-03-17 11:09:16,372] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:16,379] [INFO] DFAST_QC result json was written to OceanDNA-b10305/dqc_result.json
[2023-03-17 11:09:16,379] [INFO] DFAST_QC completed!
[2023-03-17 11:09:16,379] [INFO] Total running time: 0h1m16s