[2023-03-16 21:45:15,223] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:15,223] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:15,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference
[2023-03-16 21:45:16,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:16,469] [INFO] Task started: Prodigal
[2023-03-16 21:45:16,469] [INFO] Running command: cat /var/lib/cwl/stgac21576a-c4b4-4f83-a054-6d3e2c8ec94c/OceanDNA-b34943.fa | prodigal -d OceanDNA-b34943/cds.fna -a OceanDNA-b34943/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:28,258] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:28,259] [INFO] Task started: HMMsearch
[2023-03-16 21:45:28,259] [INFO] Running command: hmmsearch --tblout OceanDNA-b34943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/reference_markers.hmm OceanDNA-b34943/protein.faa > /dev/null
[2023-03-16 21:45:28,519] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:28,520] [INFO] Found 6/6 markers.
[2023-03-16 21:45:28,542] [INFO] Query marker FASTA was written to OceanDNA-b34943/markers.fasta
[2023-03-16 21:45:28,543] [INFO] Task started: Blastn
[2023-03-16 21:45:28,543] [INFO] Running command: blastn -query OceanDNA-b34943/markers.fasta -db /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/reference_markers.fasta -out OceanDNA-b34943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:29,204] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:29,205] [INFO] Selected 18 target genomes.
[2023-03-16 21:45:29,205] [INFO] Target genome list was writen to OceanDNA-b34943/target_genomes.txt
[2023-03-16 21:45:29,219] [INFO] Task started: fastANI
[2023-03-16 21:45:29,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgac21576a-c4b4-4f83-a054-6d3e2c8ec94c/OceanDNA-b34943.fa --refList OceanDNA-b34943/target_genomes.txt --output OceanDNA-b34943/fastani_result.tsv --threads 1
[2023-03-16 21:45:43,374] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:43,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:43,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:43,383] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:43,383] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 21:45:43,383] [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
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	87.7694	554	684	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	87.7586	557	684	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	87.6491	531	684	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=CH130	GCA_014925325.1	43657	43657	suspected-type	True	79.2615	127	684	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	79.1667	128	684	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	79.151	121	684	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	78.7582	133	684	95	below_threshold
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	78.7516	119	684	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	78.6189	136	684	95	below_threshold
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	78.6043	100	684	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	78.5162	114	684	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	78.3925	155	684	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.1757	98	684	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	78.017	114	684	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:43,383] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34943/tc_result.tsv
[2023-03-16 21:45:43,383] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:43,384] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:43,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/checkm_data
[2023-03-16 21:45:43,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:43,391] [INFO] Task started: CheckM
[2023-03-16 21:45:43,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34943/checkm_input OceanDNA-b34943/checkm_result
[2023-03-16 21:46:17,390] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:17,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.49%
Contamintation: 4.63%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:17,393] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:17,393] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:17,393] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34943/markers.fasta)
[2023-03-16 21:46:17,393] [INFO] Task started: Blastn
[2023-03-16 21:46:17,393] [INFO] Running command: blastn -query OceanDNA-b34943/markers.fasta -db /var/lib/cwl/stg22d52381-e324-4fce-bff5-8b07cbf09977/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:18,317] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:18,318] [INFO] Selected 16 target genomes.
[2023-03-16 21:46:18,318] [INFO] Target genome list was writen to OceanDNA-b34943/target_genomes_gtdb.txt
[2023-03-16 21:46:18,328] [INFO] Task started: fastANI
[2023-03-16 21:46:18,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgac21576a-c4b4-4f83-a054-6d3e2c8ec94c/OceanDNA-b34943.fa --refList OceanDNA-b34943/target_genomes_gtdb.txt --output OceanDNA-b34943/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:31,174] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:31,183] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:31,184] [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_005886345.1	s__Pseudoalteromonas phenolica_A	93.1117	619	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	88.153	551	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	87.7586	557	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_001854605.1	s__Pseudoalteromonas amylolytica	79.1667	128	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001625575.1	s__Pseudoalteromonas luteoviolacea_E	79.0532	114	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.25	97.25	0.92	0.92	2	-
GCF_018100925.1	s__Pseudoalteromonas luteoviolacea_I	79.0525	123	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	79.0471	124	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCF_014694405.1	s__Pseudoalteromonas sp014694405	78.8035	148	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854475.1	s__Pseudoalteromonas byunsanensis	78.7582	133	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886875.1	s__Pseudoalteromonas aurantia_A	78.7287	139	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.47	99.41	0.94	0.93	3	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	78.6189	136	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	78.5966	127	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_000238255.3	s__Pseudoalteromonas spongiae	78.531	113	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.31	96.27	0.89	0.86	4	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	78.4861	129	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_003590335.1	s__Pseudoalteromonas sp003590335	78.2724	147	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	78.0275	113	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:31,184] [INFO] GTDB search result was written to OceanDNA-b34943/result_gtdb.tsv
[2023-03-16 21:46:31,184] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:31,186] [INFO] DFAST_QC result json was written to OceanDNA-b34943/dqc_result.json
[2023-03-16 21:46:31,186] [INFO] DFAST_QC completed!
[2023-03-16 21:46:31,186] [INFO] Total running time: 0h1m16s