[2023-03-17 03:50:15,887] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:15,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:15,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference
[2023-03-17 03:50:17,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:17,115] [INFO] Task started: Prodigal
[2023-03-17 03:50:17,115] [INFO] Running command: cat /var/lib/cwl/stg2a36807d-3f64-4791-a517-5c29efd5014c/OceanDNA-b11352.fa | prodigal -d OceanDNA-b11352/cds.fna -a OceanDNA-b11352/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:37,356] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:37,357] [INFO] Task started: HMMsearch
[2023-03-17 03:50:37,357] [INFO] Running command: hmmsearch --tblout OceanDNA-b11352/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/reference_markers.hmm OceanDNA-b11352/protein.faa > /dev/null
[2023-03-17 03:50:37,599] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:37,600] [INFO] Found 6/6 markers.
[2023-03-17 03:50:37,620] [INFO] Query marker FASTA was written to OceanDNA-b11352/markers.fasta
[2023-03-17 03:50:37,620] [INFO] Task started: Blastn
[2023-03-17 03:50:37,620] [INFO] Running command: blastn -query OceanDNA-b11352/markers.fasta -db /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/reference_markers.fasta -out OceanDNA-b11352/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:38,240] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:38,241] [INFO] Selected 20 target genomes.
[2023-03-17 03:50:38,241] [INFO] Target genome list was writen to OceanDNA-b11352/target_genomes.txt
[2023-03-17 03:50:38,251] [INFO] Task started: fastANI
[2023-03-17 03:50:38,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a36807d-3f64-4791-a517-5c29efd5014c/OceanDNA-b11352.fa --refList OceanDNA-b11352/target_genomes.txt --output OceanDNA-b11352/fastani_result.tsv --threads 1
[2023-03-17 03:50:52,226] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:52,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:52,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:52,236] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:52,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:52,237] [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
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.4131	247	1015	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.3968	246	1015	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.3963	261	1015	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.3473	183	1015	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.2649	163	1015	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.1379	158	1015	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.873	118	1015	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.6859	111	1015	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.6854	128	1015	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.6397	92	1015	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.407	71	1015	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.2325	54	1015	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.1031	70	1015	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	75.9459	66	1015	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	75.7862	76	1015	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.737	62	1015	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	75.7184	67	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:52,237] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11352/tc_result.tsv
[2023-03-17 03:50:52,237] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:52,237] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:52,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/checkm_data
[2023-03-17 03:50:52,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:52,242] [INFO] Task started: CheckM
[2023-03-17 03:50:52,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11352/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11352/checkm_input OceanDNA-b11352/checkm_result
[2023-03-17 03:51:43,990] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:43,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:43,993] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:43,993] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:43,993] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11352/markers.fasta)
[2023-03-17 03:51:43,993] [INFO] Task started: Blastn
[2023-03-17 03:51:43,993] [INFO] Running command: blastn -query OceanDNA-b11352/markers.fasta -db /var/lib/cwl/stg34957a13-9813-4f75-95b3-483871af1b43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11352/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:44,839] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:44,840] [INFO] Selected 26 target genomes.
[2023-03-17 03:51:44,840] [INFO] Target genome list was writen to OceanDNA-b11352/target_genomes_gtdb.txt
[2023-03-17 03:51:45,107] [INFO] Task started: fastANI
[2023-03-17 03:51:45,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a36807d-3f64-4791-a517-5c29efd5014c/OceanDNA-b11352.fa --refList OceanDNA-b11352/target_genomes_gtdb.txt --output OceanDNA-b11352/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:58,395] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:58,409] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:51:58,410] [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_002813135.1	s__Altibacter sp002813135	77.4357	189	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.402	244	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.3963	261	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.3515	182	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	77.2649	163	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746845.1	s__Altibacter lentus	77.1561	156	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	77.0568	106	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_002360635.1	s__Marixanthomonas sp002360635	77.0342	150	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_011044175.1	s__Marinirhabdus sp011044175	77.0176	148	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.9945	141	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	76.994	161	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCA_002696485.1	s__Altibacter sp002696485	76.9168	142	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	99.86	99.86	0.91	0.91	2	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.8947	116	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_016757735.1	s__Aequorivita sp016757735	76.8679	118	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	76.7943	117	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043685.1	s__Pukyongia sp013043685	76.7643	92	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	-
GCF_006346335.1	s__Aequorivita sinensis	76.7026	109	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.6673	129	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106795.1	s__Aequorivita viscosa	76.6397	92	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007997135.1	s__Aequorivita lipolytica	76.5889	122	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900489465.1	s__Aequorivita sp900489465	76.5746	131	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	76.4542	98	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490835.1	s__GCA-002733185 sp015490835	76.3762	75	1015	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_000224335.1	s__Algorimicrobium argentinense	76.2325	54	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	76.1757	50	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	75.8411	67	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:58,410] [INFO] GTDB search result was written to OceanDNA-b11352/result_gtdb.tsv
[2023-03-17 03:51:58,410] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:58,412] [INFO] DFAST_QC result json was written to OceanDNA-b11352/dqc_result.json
[2023-03-17 03:51:58,412] [INFO] DFAST_QC completed!
[2023-03-17 03:51:58,412] [INFO] Total running time: 0h1m43s