[2023-03-16 20:07:31,838] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:07:31,839] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:07:31,839] [INFO] DQC Reference Directory: /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference
[2023-03-16 20:07:32,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:07:32,970] [INFO] Task started: Prodigal
[2023-03-16 20:07:32,971] [INFO] Running command: cat /var/lib/cwl/stg4cf84fc0-b999-4af8-a8e4-926d8c821f39/OceanDNA-b35309.fa | prodigal -d OceanDNA-b35309/cds.fna -a OceanDNA-b35309/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:07:54,360] [INFO] Task succeeded: Prodigal
[2023-03-16 20:07:54,360] [INFO] Task started: HMMsearch
[2023-03-16 20:07:54,360] [INFO] Running command: hmmsearch --tblout OceanDNA-b35309/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/reference_markers.hmm OceanDNA-b35309/protein.faa > /dev/null
[2023-03-16 20:07:54,593] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:07:54,593] [INFO] Found 6/6 markers.
[2023-03-16 20:07:54,617] [INFO] Query marker FASTA was written to OceanDNA-b35309/markers.fasta
[2023-03-16 20:07:54,619] [INFO] Task started: Blastn
[2023-03-16 20:07:54,619] [INFO] Running command: blastn -query OceanDNA-b35309/markers.fasta -db /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/reference_markers.fasta -out OceanDNA-b35309/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:07:55,257] [INFO] Task succeeded: Blastn
[2023-03-16 20:07:55,259] [INFO] Selected 27 target genomes.
[2023-03-16 20:07:55,259] [INFO] Target genome list was writen to OceanDNA-b35309/target_genomes.txt
[2023-03-16 20:07:55,274] [INFO] Task started: fastANI
[2023-03-16 20:07:55,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf84fc0-b999-4af8-a8e4-926d8c821f39/OceanDNA-b35309.fa --refList OceanDNA-b35309/target_genomes.txt --output OceanDNA-b35309/fastani_result.tsv --threads 1
[2023-03-16 20:08:15,104] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:15,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:08:15,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:08:15,120] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 20:08:15,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 20:08:15,120] [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
Vibrio caribbeanicus	strain=ATCC BAA-2122	GCA_000165125.2	701175	701175	type	True	96.3423	1159	1305	95	conclusive
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.0742	233	1305	95	below_threshold
Vibrio pacinii	strain=DSM 19139	GCA_000711795.1	170674	170674	type	True	78.9089	210	1305	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	78.8699	253	1305	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.8484	238	1305	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	78.8006	249	1305	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	78.7248	224	1305	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	78.6846	236	1305	95	below_threshold
Vibrio salilacus	strain=DSG-S6	GCA_002811245.1	1323749	1323749	type	True	78.6766	202	1305	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	78.6167	213	1305	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	78.6058	214	1305	95	below_threshold
Vibrio ostreicida	strain=PP-203	GCA_013074385.2	526588	526588	type	True	78.3561	171	1305	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	78.3493	203	1305	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	78.2253	191	1305	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.1773	154	1305	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	78.1687	192	1305	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	78.1219	167	1305	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	78.0674	115	1305	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	78.0571	170	1305	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	77.9944	134	1305	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	77.7822	87	1305	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	77.7012	131	1305	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	77.5939	141	1305	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	77.551	83	1305	95	below_threshold
Vibrio gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	77.332	154	1305	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	77.2985	160	1305	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:08:15,121] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35309/tc_result.tsv
[2023-03-16 20:08:15,121] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:08:15,121] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:08:15,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/checkm_data
[2023-03-16 20:08:15,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:08:15,129] [INFO] Task started: CheckM
[2023-03-16 20:08:15,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35309/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35309/checkm_input OceanDNA-b35309/checkm_result
[2023-03-16 20:09:22,479] [INFO] Task succeeded: CheckM
[2023-03-16 20:09:22,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:09:22,483] [INFO] ===== Completeness check finished =====
[2023-03-16 20:09:22,483] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:09:22,483] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35309/markers.fasta)
[2023-03-16 20:09:22,488] [INFO] Task started: Blastn
[2023-03-16 20:09:22,488] [INFO] Running command: blastn -query OceanDNA-b35309/markers.fasta -db /var/lib/cwl/stga3ea11cb-d104-4e0e-819e-59cd552f9694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35309/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:09:23,827] [INFO] Task succeeded: Blastn
[2023-03-16 20:09:23,830] [INFO] Selected 24 target genomes.
[2023-03-16 20:09:23,830] [INFO] Target genome list was writen to OceanDNA-b35309/target_genomes_gtdb.txt
[2023-03-16 20:09:23,856] [INFO] Task started: fastANI
[2023-03-16 20:09:23,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cf84fc0-b999-4af8-a8e4-926d8c821f39/OceanDNA-b35309.fa --refList OceanDNA-b35309/target_genomes_gtdb.txt --output OceanDNA-b35309/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:09:53,317] [INFO] Task succeeded: fastANI
[2023-03-16 20:09:53,331] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:09:53,332] [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_000165125.1	s__Vibrio caribbeanicus	96.3423	1159	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000189255.1	s__Vibrio brasiliensis	78.9975	252	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711795.1	s__Vibrio pacinii	78.91	209	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_000772105.1	s__Vibrio tubiashii	78.894	251	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_001399455.2	s__Vibrio bivalvicida	78.8067	248	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_013113835.1	s__Vibrio sp013113835	78.7177	207	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811245.1	s__Vibrio salilacus	78.6869	202	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.5386	N/A	N/A	N/A	N/A	1	-
GCF_013114545.1	s__Vibrio sp013114545	78.6756	216	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	78.6729	223	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967545.1	s__Vibrio galatheae	78.6465	238	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176135.1	s__Vibrio coralliilyticus	78.6339	211	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_003970385.1	s__Vibrio aquaticus	78.6058	214	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	78.4601	216	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_001854765.1	s__Vibrio sonorensis	78.2927	139	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591105.1	s__Vibrio nereis	78.238	191	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003937805.1	s__Vibrio pectenicida	78.238	197	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.20	98.20	0.85	0.85	2	-
GCF_014050145.1	s__Vibrio marinisediminis	78.1966	152	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400365.1	s__Vibrio jasicida	78.1911	172	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_018860525.1	s__Vibrio hepatarius_B	78.157	191	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000830505.1	s__Vibrio mytili	78.0783	159	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064285.1	s__Vibrio ziniensis	78.0097	135	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970425.1	s__Vibrio penaeicida	77.6994	129	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_002877365.1	s__Vibrio sp002877365	77.656	133	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281825.1	s__Vibrio gallaecicus	77.2752	155	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:09:53,332] [INFO] GTDB search result was written to OceanDNA-b35309/result_gtdb.tsv
[2023-03-16 20:09:53,332] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:09:53,335] [INFO] DFAST_QC result json was written to OceanDNA-b35309/dqc_result.json
[2023-03-16 20:09:53,335] [INFO] DFAST_QC completed!
[2023-03-16 20:09:53,335] [INFO] Total running time: 0h2m21s