[2023-03-19 02:40:15,841] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,841] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference
[2023-03-19 02:40:17,559] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,563] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,563] [INFO] Running command: cat /var/lib/cwl/stgb056cbe4-dc53-4019-b29e-4e92b31d8578/OceanDNA-b10294.fa | prodigal -d OceanDNA-b10294/cds.fna -a OceanDNA-b10294/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:47,892] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:47,893] [INFO] Task started: HMMsearch
[2023-03-19 02:40:47,893] [INFO] Running command: hmmsearch --tblout OceanDNA-b10294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/reference_markers.hmm OceanDNA-b10294/protein.faa > /dev/null
[2023-03-19 02:40:48,129] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:48,129] [INFO] Found 6/6 markers.
[2023-03-19 02:40:48,156] [INFO] Query marker FASTA was written to OceanDNA-b10294/markers.fasta
[2023-03-19 02:40:48,157] [INFO] Task started: Blastn
[2023-03-19 02:40:48,157] [INFO] Running command: blastn -query OceanDNA-b10294/markers.fasta -db /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/reference_markers.fasta -out OceanDNA-b10294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:48,777] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:48,781] [INFO] Selected 25 target genomes.
[2023-03-19 02:40:48,781] [INFO] Target genome list was writen to OceanDNA-b10294/target_genomes.txt
[2023-03-19 02:40:48,799] [INFO] Task started: fastANI
[2023-03-19 02:40:48,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgb056cbe4-dc53-4019-b29e-4e92b31d8578/OceanDNA-b10294.fa --refList OceanDNA-b10294/target_genomes.txt --output OceanDNA-b10294/fastani_result.tsv --threads 1
[2023-03-19 02:41:02,455] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:02,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:41:02,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:41:02,469] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:41:02,469] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:41:02,469] [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 holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	77.5033	117	1383	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	77.1795	121	1383	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	77.0933	130	1383	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	76.9603	123	1383	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	76.8935	141	1383	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	76.875	139	1383	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.8428	144	1383	95	below_threshold
Tenacibaculum maritimum		GCA_900119795.1	107401	107401	type	True	76.8226	97	1383	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.781	141	1383	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.6326	126	1383	95	below_threshold
Tenacibaculum skagerrakense	strain=DSM 14836	GCA_004345825.1	186571	186571	type	True	76.6271	123	1383	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.6262	152	1383	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.6244	102	1383	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.6068	158	1383	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	76.5534	121	1383	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.5391	111	1383	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.4061	136	1383	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.405	136	1383	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.405	136	1383	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.3962	150	1383	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	76.3895	148	1383	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.2752	113	1383	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.2546	144	1383	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:41:02,470] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10294/tc_result.tsv
[2023-03-19 02:41:02,471] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:41:02,471] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:41:02,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/checkm_data
[2023-03-19 02:41:02,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:41:02,480] [INFO] Task started: CheckM
[2023-03-19 02:41:02,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10294/checkm_input OceanDNA-b10294/checkm_result
[2023-03-19 02:42:18,755] [INFO] Task succeeded: CheckM
[2023-03-19 02:42:18,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:42:18,863] [INFO] ===== Completeness check finished =====
[2023-03-19 02:42:18,863] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:42:18,863] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10294/markers.fasta)
[2023-03-19 02:42:18,864] [INFO] Task started: Blastn
[2023-03-19 02:42:18,864] [INFO] Running command: blastn -query OceanDNA-b10294/markers.fasta -db /var/lib/cwl/stg369fedea-b55d-4ad8-bb2c-4b2bf3f9fbc4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:42:19,875] [INFO] Task succeeded: Blastn
[2023-03-19 02:42:19,877] [INFO] Selected 30 target genomes.
[2023-03-19 02:42:19,877] [INFO] Target genome list was writen to OceanDNA-b10294/target_genomes_gtdb.txt
[2023-03-19 02:42:19,932] [INFO] Task started: fastANI
[2023-03-19 02:42:19,932] [INFO] Running command: fastANI --query /var/lib/cwl/stgb056cbe4-dc53-4019-b29e-4e92b31d8578/OceanDNA-b10294.fa --refList OceanDNA-b10294/target_genomes_gtdb.txt --output OceanDNA-b10294/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:42:34,926] [INFO] Task succeeded: fastANI
[2023-03-19 02:42:34,943] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:42:34,943] [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
GCF_002120225.1	s__Tenacibaculum holothuriorum	77.5033	117	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	77.2024	120	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	77.1129	129	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387615.1	s__Tenacibaculum gallaicum	76.9799	122	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105455.1	s__Tenacibaculum sp900105455	76.9391	119	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763215.1	s__SCGC-AAA160-P02 sp016763215	76.8964	136	1383	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_003867075.1	s__Tenacibaculum mesophilum	76.8935	141	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	76.8901	152	1383	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	-
GCA_018663625.1	s__Polaribacter sp018663625	76.8614	105	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_900119795.1	s__Tenacibaculum maritimum	76.8478	96	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.84	97.91	0.93	0.90	25	-
GCA_013214275.1	s__SCGC-AAA160-P02 sp013214275	76.8385	107	1383	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	76.8076	130	1383	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	-
GCF_009832745.1	s__Polaribacter sp009832745	76.7647	142	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	76.7554	118	1383	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	76.7052	146	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	76.6784	132	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345825.1	s__Tenacibaculum skagerrakense	76.6451	122	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.639	151	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954645.1	s__Polaribacter gangjinensis	76.6217	143	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	76.6098	122	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	76.5799	116	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	76.5532	118	1383	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	76.5391	111	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	76.5331	97	1383	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_007827455.1	s__VISM01 sp007827455	76.4983	161	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005425.1	s__Polaribacter sp002005425	76.4964	120	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.405	136	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	76.4026	147	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004762155.1	s__Tenacibaculum sp004762155	76.1231	130	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763595.1	s__Polaribacter_A sp016763595	75.7882	65	1383	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:42:34,948] [INFO] GTDB search result was written to OceanDNA-b10294/result_gtdb.tsv
[2023-03-19 02:42:34,958] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:42:34,965] [INFO] DFAST_QC result json was written to OceanDNA-b10294/dqc_result.json
[2023-03-19 02:42:34,966] [INFO] DFAST_QC completed!
[2023-03-19 02:42:34,966] [INFO] Total running time: 0h2m19s