[2023-03-16 10:35:17,651] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:17,651] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:17,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference
[2023-03-16 10:35:18,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:18,777] [INFO] Task started: Prodigal
[2023-03-16 10:35:18,777] [INFO] Running command: cat /var/lib/cwl/stg08314e06-7852-4195-a793-fba48f300ac5/OceanDNA-b9812.fa | prodigal -d OceanDNA-b9812/cds.fna -a OceanDNA-b9812/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:32,235] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:32,236] [INFO] Task started: HMMsearch
[2023-03-16 10:35:32,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b9812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/reference_markers.hmm OceanDNA-b9812/protein.faa > /dev/null
[2023-03-16 10:35:32,483] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:32,484] [INFO] Found 6/6 markers.
[2023-03-16 10:35:32,500] [INFO] Query marker FASTA was written to OceanDNA-b9812/markers.fasta
[2023-03-16 10:35:32,501] [INFO] Task started: Blastn
[2023-03-16 10:35:32,502] [INFO] Running command: blastn -query OceanDNA-b9812/markers.fasta -db /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/reference_markers.fasta -out OceanDNA-b9812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:33,188] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:33,189] [INFO] Selected 26 target genomes.
[2023-03-16 10:35:33,189] [INFO] Target genome list was writen to OceanDNA-b9812/target_genomes.txt
[2023-03-16 10:35:33,200] [INFO] Task started: fastANI
[2023-03-16 10:35:33,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg08314e06-7852-4195-a793-fba48f300ac5/OceanDNA-b9812.fa --refList OceanDNA-b9812/target_genomes.txt --output OceanDNA-b9812/fastani_result.tsv --threads 1
[2023-03-16 10:35:50,020] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:50,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:50,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:50,033] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:50,034] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:35:50,034] [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 septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.9668	136	591	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	76.7065	79	591	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.5189	121	591	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.4645	129	591	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	76.4622	90	591	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.4496	139	591	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.4425	107	591	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.4362	139	591	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.4321	104	591	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.4156	117	591	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.4117	94	591	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.3978	115	591	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.3937	116	591	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	76.3877	135	591	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	76.2827	89	591	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.201	87	591	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.1547	119	591	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	76.1509	80	591	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	76.14	94	591	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.0458	111	591	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	75.9505	87	591	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	75.4268	57	591	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:35:50,034] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9812/tc_result.tsv
[2023-03-16 10:35:50,034] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:50,034] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:50,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/checkm_data
[2023-03-16 10:35:50,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:50,039] [INFO] Task started: CheckM
[2023-03-16 10:35:50,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9812/checkm_input OceanDNA-b9812/checkm_result
[2023-03-16 10:36:29,233] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:29,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.59%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:29,242] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:29,242] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:29,242] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9812/markers.fasta)
[2023-03-16 10:36:29,244] [INFO] Task started: Blastn
[2023-03-16 10:36:29,244] [INFO] Running command: blastn -query OceanDNA-b9812/markers.fasta -db /var/lib/cwl/stgdb2f82af-c3ac-4d64-a7d9-44a472eba083/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:30,205] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:30,206] [INFO] Selected 27 target genomes.
[2023-03-16 10:36:30,206] [INFO] Target genome list was writen to OceanDNA-b9812/target_genomes_gtdb.txt
[2023-03-16 10:36:30,245] [INFO] Task started: fastANI
[2023-03-16 10:36:30,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg08314e06-7852-4195-a793-fba48f300ac5/OceanDNA-b9812.fa --refList OceanDNA-b9812/target_genomes_gtdb.txt --output OceanDNA-b9812/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:36:45,671] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:45,685] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:36:45,685] [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	77.9028	265	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009832745.1	s__Polaribacter sp009832745	76.9668	136	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124875.1	s__Tenacibaculum adriaticum	76.7363	78	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	76.6725	106	591	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	76.6123	114	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	76.5998	104	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	76.5871	122	591	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	76.5529	131	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954605.1	s__Polaribacter butkevichii	76.5527	104	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	76.5189	121	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	76.4714	107	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.4645	129	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	76.4425	107	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001975665.1	s__Polaribacter reichenbachii	76.4305	137	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_016858305.2	s__Polaribacter sp016858305	76.4145	102	591	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	76.3937	116	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019263805.1	s__Polaribacter sp011379025	76.3725	116	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_004337695.1	s__Tenacibaculum sp004337695	76.2207	85	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663625.1	s__Polaribacter sp018663625	76.1541	83	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	76.1509	80	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	76.0458	111	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831685.1	s__Polaribacter sp002831685	76.0057	103	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	75.9505	87	591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:36:45,685] [INFO] GTDB search result was written to OceanDNA-b9812/result_gtdb.tsv
[2023-03-16 10:36:45,686] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:36:45,688] [INFO] DFAST_QC result json was written to OceanDNA-b9812/dqc_result.json
[2023-03-16 10:36:45,688] [INFO] DFAST_QC completed!
[2023-03-16 10:36:45,688] [INFO] Total running time: 0h1m28s