[2023-03-16 20:07:31,822] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:07:31,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:07:31,822] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference
[2023-03-16 20:07:33,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:07:33,015] [INFO] Task started: Prodigal
[2023-03-16 20:07:33,016] [INFO] Running command: cat /var/lib/cwl/stg7268eb86-e89f-4f18-867c-cb79213eaf86/OceanDNA-b7431.fa | prodigal -d OceanDNA-b7431/cds.fna -a OceanDNA-b7431/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:07:44,784] [INFO] Task succeeded: Prodigal
[2023-03-16 20:07:44,785] [INFO] Task started: HMMsearch
[2023-03-16 20:07:44,785] [INFO] Running command: hmmsearch --tblout OceanDNA-b7431/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/reference_markers.hmm OceanDNA-b7431/protein.faa > /dev/null
[2023-03-16 20:07:44,975] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:07:44,975] [INFO] Found 6/6 markers.
[2023-03-16 20:07:44,990] [INFO] Query marker FASTA was written to OceanDNA-b7431/markers.fasta
[2023-03-16 20:07:44,991] [INFO] Task started: Blastn
[2023-03-16 20:07:44,992] [INFO] Running command: blastn -query OceanDNA-b7431/markers.fasta -db /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/reference_markers.fasta -out OceanDNA-b7431/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:07:45,593] [INFO] Task succeeded: Blastn
[2023-03-16 20:07:45,595] [INFO] Selected 30 target genomes.
[2023-03-16 20:07:45,595] [INFO] Target genome list was writen to OceanDNA-b7431/target_genomes.txt
[2023-03-16 20:07:45,616] [INFO] Task started: fastANI
[2023-03-16 20:07:45,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg7268eb86-e89f-4f18-867c-cb79213eaf86/OceanDNA-b7431.fa --refList OceanDNA-b7431/target_genomes.txt --output OceanDNA-b7431/fastani_result.tsv --threads 1
[2023-03-16 20:08:01,777] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:01,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:08:01,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:08:01,791] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:08:01,791] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:08:01,791] [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
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.5139	50	592	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.4105	77	592	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.4105	77	592	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	76.2869	61	592	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.2779	84	592	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.2074	50	592	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.2012	78	592	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.1983	74	592	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.187	57	592	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.1654	75	592	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.1137	52	592	95	below_threshold
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	76.1105	62	592	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.1018	64	592	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.0972	65	592	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.0822	64	592	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.0734	69	592	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	76.0458	50	592	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	75.9619	56	592	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	75.9591	86	592	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	75.9582	70	592	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.9298	62	592	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	75.9139	72	592	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	75.8489	57	592	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	75.8083	56	592	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	75.7411	61	592	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:08:01,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7431/tc_result.tsv
[2023-03-16 20:08:01,793] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:08:01,793] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:08:01,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/checkm_data
[2023-03-16 20:08:01,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:08:01,799] [INFO] Task started: CheckM
[2023-03-16 20:08:01,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7431/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7431/checkm_input OceanDNA-b7431/checkm_result
[2023-03-16 20:08:34,287] [INFO] Task succeeded: CheckM
[2023-03-16 20:08:34,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:08:34,289] [INFO] ===== Completeness check finished =====
[2023-03-16 20:08:34,289] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:08:34,289] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7431/markers.fasta)
[2023-03-16 20:08:34,291] [INFO] Task started: Blastn
[2023-03-16 20:08:34,291] [INFO] Running command: blastn -query OceanDNA-b7431/markers.fasta -db /var/lib/cwl/stgf0d87bf7-80b2-4a06-99db-d2f3c2efcf8b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7431/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:08:35,143] [INFO] Task succeeded: Blastn
[2023-03-16 20:08:35,144] [INFO] Selected 12 target genomes.
[2023-03-16 20:08:35,144] [INFO] Target genome list was writen to OceanDNA-b7431/target_genomes_gtdb.txt
[2023-03-16 20:08:35,157] [INFO] Task started: fastANI
[2023-03-16 20:08:35,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg7268eb86-e89f-4f18-867c-cb79213eaf86/OceanDNA-b7431.fa --refList OceanDNA-b7431/target_genomes_gtdb.txt --output OceanDNA-b7431/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:08:41,231] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:41,240] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:08:41,240] [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
GCA_018608625.1	s__Hel1-33-131 sp018608625	99.8179	519	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	conclusive
GCA_905181825.1	s__Hel1-33-131 sp905181825	83.6122	387	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	83.3115	426	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	78.7903	268	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	78.698	291	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	78.4905	237	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	78.3774	229	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	78.3103	263	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	78.0832	183	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	76.1983	74	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCA_905479815.1	s__Psychroserpens sp905479815	75.9762	67	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217215.1	s__Winogradskyella epiphytica	75.8489	57	592	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:08:41,240] [INFO] GTDB search result was written to OceanDNA-b7431/result_gtdb.tsv
[2023-03-16 20:08:41,241] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:08:41,243] [INFO] DFAST_QC result json was written to OceanDNA-b7431/dqc_result.json
[2023-03-16 20:08:41,243] [INFO] DFAST_QC completed!
[2023-03-16 20:08:41,243] [INFO] Total running time: 0h1m9s