[2023-03-15 23:07:02,659] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,659] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,967] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stgcedebe7e-a9b9-49d7-a60c-242759f6d5d3/OceanDNA-b35312.fa | prodigal -d OceanDNA-b35312/cds.fna -a OceanDNA-b35312/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:27,429] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:27,429] [INFO] Task started: HMMsearch
[2023-03-15 23:07:27,430] [INFO] Running command: hmmsearch --tblout OceanDNA-b35312/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/reference_markers.hmm OceanDNA-b35312/protein.faa > /dev/null
[2023-03-15 23:07:27,671] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:27,671] [INFO] Found 6/6 markers.
[2023-03-15 23:07:27,696] [INFO] Query marker FASTA was written to OceanDNA-b35312/markers.fasta
[2023-03-15 23:07:27,698] [INFO] Task started: Blastn
[2023-03-15 23:07:27,698] [INFO] Running command: blastn -query OceanDNA-b35312/markers.fasta -db /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/reference_markers.fasta -out OceanDNA-b35312/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:28,476] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:28,476] [INFO] Selected 20 target genomes.
[2023-03-15 23:07:28,477] [INFO] Target genome list was writen to OceanDNA-b35312/target_genomes.txt
[2023-03-15 23:07:28,556] [INFO] Task started: fastANI
[2023-03-15 23:07:28,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedebe7e-a9b9-49d7-a60c-242759f6d5d3/OceanDNA-b35312.fa --refList OceanDNA-b35312/target_genomes.txt --output OceanDNA-b35312/fastani_result.tsv --threads 1
[2023-03-15 23:07:49,286] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:49,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:49,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:49,299] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 23:07:49,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 23:07:49,299] [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 cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	99.1514	1337	1408	95	conclusive
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	89.3321	1137	1408	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	89.3264	1148	1408	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.325	1174	1408	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	89.3047	1239	1408	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.0377	1199	1408	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	88.7942	1174	1408	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	88.5779	1109	1408	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	88.5742	1103	1408	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	88.5327	1114	1408	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	88.5013	1103	1408	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	88.3528	1172	1408	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	88.1302	1225	1408	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	88.0747	1149	1408	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	88.0256	1092	1408	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	88.0159	1088	1408	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	87.9283	1179	1408	95	below_threshold
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	87.7623	1096	1408	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	87.7561	1110	1408	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	87.7167	1110	1408	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:49,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35312/tc_result.tsv
[2023-03-15 23:07:49,316] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:49,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:49,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/checkm_data
[2023-03-15 23:07:49,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:49,323] [INFO] Task started: CheckM
[2023-03-15 23:07:49,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35312/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35312/checkm_input OceanDNA-b35312/checkm_result
[2023-03-15 23:08:48,377] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:48,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:48,515] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:48,515] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:48,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35312/markers.fasta)
[2023-03-15 23:08:48,517] [INFO] Task started: Blastn
[2023-03-15 23:08:48,517] [INFO] Running command: blastn -query OceanDNA-b35312/markers.fasta -db /var/lib/cwl/stg95a0dd4e-8e68-4a3b-a9e7-d45dae6392e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35312/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:49,619] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:49,624] [INFO] Selected 19 target genomes.
[2023-03-15 23:08:49,625] [INFO] Target genome list was writen to OceanDNA-b35312/target_genomes_gtdb.txt
[2023-03-15 23:08:49,634] [INFO] Task started: fastANI
[2023-03-15 23:08:49,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedebe7e-a9b9-49d7-a60c-242759f6d5d3/OceanDNA-b35312.fa --refList OceanDNA-b35312/target_genomes_gtdb.txt --output OceanDNA-b35312/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:09:09,799] [INFO] Task succeeded: fastANI
[2023-03-15 23:09:09,810] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:09:09,810] [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_005144905.1	s__Vibrio cyclitrophicus	99.3676	1350	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	conclusive
GCF_000272045.2	s__Vibrio crassostreae_C	89.4552	1197	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002156525.1	s__Vibrio celticus	89.3449	1135	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_002156455.1	s__Vibrio coralliirubri	89.2338	1149	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_000272105.2	s__Vibrio splendidus_I	89.2113	1143	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	88.7942	1174	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_002875945.1	s__Vibrio lentus_A	88.7831	1183	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858795.1	s__Vibrio sp007858795	88.6642	1172	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557875.1	s__Vibrio splendidus_F	88.656	1161	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_900089855.1	s__Vibrio atlanticus	88.5779	1109	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	88.5585	1060	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_000316985.1	s__Vibrio sp000316985	88.5244	1107	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	88.5069	1139	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_006333845.1	s__Vibrio tasmaniensis	88.503	1102	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_013394185.1	s__Vibrio sp013394185	88.421	1186	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014879975.1	s__Vibrio bathopelagicus	88.3528	1172	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156475.1	s__Vibrio gigantis	88.0695	1150	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_008801285.1	s__Vibrio kanaloae	88.0344	1091	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_900089765.1	s__Vibrio toranzoniae	87.7096	1111	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	-
--------------------------------------------------------------------------------
[2023-03-15 23:09:09,814] [INFO] GTDB search result was written to OceanDNA-b35312/result_gtdb.tsv
[2023-03-15 23:09:09,814] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:09:09,819] [INFO] DFAST_QC result json was written to OceanDNA-b35312/dqc_result.json
[2023-03-15 23:09:09,819] [INFO] DFAST_QC completed!
[2023-03-15 23:09:09,820] [INFO] Total running time: 0h2m7s