[2023-03-14 12:25:41,577] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,577] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference
[2023-03-14 12:25:42,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,813] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,813] [INFO] Running command: cat /var/lib/cwl/stgffdb49a1-2c29-4c34-924a-34be3dc8aab8/OceanDNA-b35289.fa | prodigal -d OceanDNA-b35289/cds.fna -a OceanDNA-b35289/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:46,093] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:46,093] [INFO] Task started: HMMsearch
[2023-03-14 12:25:46,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b35289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/reference_markers.hmm OceanDNA-b35289/protein.faa > /dev/null
[2023-03-14 12:25:46,223] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:46,224] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgffdb49a1-2c29-4c34-924a-34be3dc8aab8/OceanDNA-b35289.fa]
[2023-03-14 12:25:46,230] [INFO] Query marker FASTA was written to OceanDNA-b35289/markers.fasta
[2023-03-14 12:25:46,230] [INFO] Task started: Blastn
[2023-03-14 12:25:46,230] [INFO] Running command: blastn -query OceanDNA-b35289/markers.fasta -db /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/reference_markers.fasta -out OceanDNA-b35289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:46,753] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:46,753] [INFO] Selected 11 target genomes.
[2023-03-14 12:25:46,754] [INFO] Target genome list was writen to OceanDNA-b35289/target_genomes.txt
[2023-03-14 12:25:46,761] [INFO] Task started: fastANI
[2023-03-14 12:25:46,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdb49a1-2c29-4c34-924a-34be3dc8aab8/OceanDNA-b35289.fa --refList OceanDNA-b35289/target_genomes.txt --output OceanDNA-b35289/fastani_result.tsv --threads 1
[2023-03-14 12:25:54,738] [INFO] Task succeeded: fastANI
[2023-03-14 12:25:54,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:25:54,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:25:54,746] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2023-03-14 12:25:54,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:25:54,747] [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 gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	98.2709	196	202	95	conclusive
Vibrio gallaecicus	strain=DSM 23502	GCA_005281825.1	552386	552386	type	True	98.2709	196	202	95	conclusive
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	98.1858	196	202	95	conclusive
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	86.1152	155	202	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	85.8628	153	202	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	85.8021	153	202	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	85.5586	157	202	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	85.557	153	202	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	85.3508	157	202	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	85.2424	152	202	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	83.6543	139	202	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:25:54,747] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35289/tc_result.tsv
[2023-03-14 12:25:54,747] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:25:54,747] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:54,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/checkm_data
[2023-03-14 12:25:54,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:54,755] [INFO] Task started: CheckM
[2023-03-14 12:25:54,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35289/checkm_input OceanDNA-b35289/checkm_result
[2023-03-14 12:26:09,575] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:09,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:09,576] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:09,576] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:09,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35289/markers.fasta)
[2023-03-14 12:26:09,577] [INFO] Task started: Blastn
[2023-03-14 12:26:09,577] [INFO] Running command: blastn -query OceanDNA-b35289/markers.fasta -db /var/lib/cwl/stgbe758d94-c3de-4239-83a4-0a72a3560068/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:10,107] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:10,108] [INFO] Selected 15 target genomes.
[2023-03-14 12:26:10,108] [INFO] Target genome list was writen to OceanDNA-b35289/target_genomes_gtdb.txt
[2023-03-14 12:26:10,129] [INFO] Task started: fastANI
[2023-03-14 12:26:10,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgffdb49a1-2c29-4c34-924a-34be3dc8aab8/OceanDNA-b35289.fa --refList OceanDNA-b35289/target_genomes_gtdb.txt --output OceanDNA-b35289/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:21,230] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:21,239] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:26:21,239] [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_005281825.1	s__Vibrio gallaecicus	98.2709	196	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013114625.1	s__Vibrio sp013114625	92.9461	188	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014879975.1	s__Vibrio bathopelagicus	85.8628	153	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006333845.1	s__Vibrio tasmaniensis	85.8279	150	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_001557875.1	s__Vibrio splendidus_F	85.7324	155	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_014878155.1	s__Vibrio lentus	85.7178	159	202	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	85.7165	162	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	85.5971	151	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_900089855.1	s__Vibrio atlanticus	85.557	153	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	85.4493	154	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_004764665.1	s__Vibrio echinoideorum	85.4174	156	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_008801285.1	s__Vibrio kanaloae	85.2685	151	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_005144905.1	s__Vibrio cyclitrophicus	85.2415	157	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	-
GCF_002954585.1	s__Vibrio chagasii_A	84.5424	151	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_005281835.1	s__Vibrio profundi	83.6543	139	202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:21,240] [INFO] GTDB search result was written to OceanDNA-b35289/result_gtdb.tsv
[2023-03-14 12:26:21,240] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:21,241] [INFO] DFAST_QC result json was written to OceanDNA-b35289/dqc_result.json
[2023-03-14 12:26:21,241] [INFO] DFAST_QC completed!
[2023-03-14 12:26:21,241] [INFO] Total running time: 0h0m40s