[2023-03-15 12:13:55,703] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:13:55,704] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:13:55,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference
[2023-03-15 12:13:57,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:13:57,410] [INFO] Task started: Prodigal
[2023-03-15 12:13:57,410] [INFO] Running command: cat /var/lib/cwl/stg7bb79b8b-3047-44f8-9d11-33718ae89970/OceanDNA-b7010.fa | prodigal -d OceanDNA-b7010/cds.fna -a OceanDNA-b7010/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:14:08,460] [INFO] Task succeeded: Prodigal
[2023-03-15 12:14:08,460] [INFO] Task started: HMMsearch
[2023-03-15 12:14:08,460] [INFO] Running command: hmmsearch --tblout OceanDNA-b7010/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/reference_markers.hmm OceanDNA-b7010/protein.faa > /dev/null
[2023-03-15 12:14:08,650] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:14:08,651] [INFO] Found 6/6 markers.
[2023-03-15 12:14:08,673] [INFO] Query marker FASTA was written to OceanDNA-b7010/markers.fasta
[2023-03-15 12:14:08,673] [INFO] Task started: Blastn
[2023-03-15 12:14:08,673] [INFO] Running command: blastn -query OceanDNA-b7010/markers.fasta -db /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/reference_markers.fasta -out OceanDNA-b7010/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:14:09,261] [INFO] Task succeeded: Blastn
[2023-03-15 12:14:09,265] [INFO] Selected 37 target genomes.
[2023-03-15 12:14:09,266] [INFO] Target genome list was writen to OceanDNA-b7010/target_genomes.txt
[2023-03-15 12:14:09,315] [INFO] Task started: fastANI
[2023-03-15 12:14:09,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb79b8b-3047-44f8-9d11-33718ae89970/OceanDNA-b7010.fa --refList OceanDNA-b7010/target_genomes.txt --output OceanDNA-b7010/fastani_result.tsv --threads 1
[2023-03-15 12:14:29,896] [INFO] Task succeeded: fastANI
[2023-03-15 12:14:29,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:14:29,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:14:29,915] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:14:29,915] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:14:29,916] [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
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	77.157	84	572	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.9227	86	572	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.7129	70	572	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.6787	72	572	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.6711	75	572	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.6581	65	572	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.5592	73	572	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.5444	94	572	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.5262	67	572	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.5129	66	572	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.5129	66	572	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	76.5032	54	572	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.4996	68	572	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.4881	88	572	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.4838	96	572	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.4473	112	572	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.4447	80	572	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.3834	69	572	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.3723	69	572	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.3689	88	572	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.3186	72	572	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.2901	69	572	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	76.286	67	572	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.258	76	572	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.225	52	572	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	76.2103	76	572	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.1604	72	572	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.0969	69	572	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.0587	82	572	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.0563	96	572	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.0345	74	572	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0146	57	572	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.9799	70	572	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	75.9426	64	572	95	below_threshold
Tenacibaculum adriaticum	strain=DSM 18961	GCA_008124875.1	413713	413713	type	True	75.9029	77	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:14:29,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7010/tc_result.tsv
[2023-03-15 12:14:29,920] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:14:29,920] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:14:29,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/checkm_data
[2023-03-15 12:14:29,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:14:29,926] [INFO] Task started: CheckM
[2023-03-15 12:14:29,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7010/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7010/checkm_input OceanDNA-b7010/checkm_result
[2023-03-15 12:15:01,655] [INFO] Task succeeded: CheckM
[2023-03-15 12:15:01,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:15:01,700] [INFO] ===== Completeness check finished =====
[2023-03-15 12:15:01,701] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:15:01,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7010/markers.fasta)
[2023-03-15 12:15:01,702] [INFO] Task started: Blastn
[2023-03-15 12:15:01,702] [INFO] Running command: blastn -query OceanDNA-b7010/markers.fasta -db /var/lib/cwl/stg90793150-2b87-4ff7-9ac7-40b34b44f5f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7010/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:15:02,544] [INFO] Task succeeded: Blastn
[2023-03-15 12:15:02,572] [INFO] Selected 10 target genomes.
[2023-03-15 12:15:02,572] [INFO] Target genome list was writen to OceanDNA-b7010/target_genomes_gtdb.txt
[2023-03-15 12:15:02,747] [INFO] Task started: fastANI
[2023-03-15 12:15:02,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bb79b8b-3047-44f8-9d11-33718ae89970/OceanDNA-b7010.fa --refList OceanDNA-b7010/target_genomes_gtdb.txt --output OceanDNA-b7010/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:15:07,593] [INFO] Task succeeded: fastANI
[2023-03-15 12:15:07,600] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:15:07,600] [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_002713705.1	s__GCA-002733185 sp002713705	93.4831	541	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_018669795.1	s__GCA-002733185 sp018669795	91.1518	510	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_905181835.1	s__GCA-002733185 sp905181835	79.1185	277	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	78.7114	242	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	78.4082	191	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_004214175.1	s__GCA-002733185 sp004214175	78.217	179	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	77.303	141	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013285155.1	s__Winogradskyella undariae	76.9227	86	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_900106795.1	s__Aequorivita viscosa	76.5129	66	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002390165.1	s__Lutibacter sp002390165	75.6233	65	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:15:07,610] [INFO] GTDB search result was written to OceanDNA-b7010/result_gtdb.tsv
[2023-03-15 12:15:07,627] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:15:07,638] [INFO] DFAST_QC result json was written to OceanDNA-b7010/dqc_result.json
[2023-03-15 12:15:07,638] [INFO] DFAST_QC completed!
[2023-03-15 12:15:07,638] [INFO] Total running time: 0h1m12s