[2023-03-18 20:13:32,249] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,250] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference
[2023-03-18 20:13:33,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,435] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,435] [INFO] Running command: cat /var/lib/cwl/stg29fd1980-b778-464e-a484-56c0c3e6f304/OceanDNA-b6696.fa | prodigal -d OceanDNA-b6696/cds.fna -a OceanDNA-b6696/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:50,554] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:50,554] [INFO] Task started: HMMsearch
[2023-03-18 20:13:50,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b6696/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/reference_markers.hmm OceanDNA-b6696/protein.faa > /dev/null
[2023-03-18 20:13:50,781] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:50,782] [INFO] Found 6/6 markers.
[2023-03-18 20:13:50,799] [INFO] Query marker FASTA was written to OceanDNA-b6696/markers.fasta
[2023-03-18 20:13:50,800] [INFO] Task started: Blastn
[2023-03-18 20:13:50,800] [INFO] Running command: blastn -query OceanDNA-b6696/markers.fasta -db /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/reference_markers.fasta -out OceanDNA-b6696/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:51,452] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:51,452] [INFO] Selected 25 target genomes.
[2023-03-18 20:13:51,453] [INFO] Target genome list was writen to OceanDNA-b6696/target_genomes.txt
[2023-03-18 20:13:51,463] [INFO] Task started: fastANI
[2023-03-18 20:13:51,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg29fd1980-b778-464e-a484-56c0c3e6f304/OceanDNA-b6696.fa --refList OceanDNA-b6696/target_genomes.txt --output OceanDNA-b6696/fastani_result.tsv --threads 1
[2023-03-18 20:14:06,867] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:06,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:06,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:06,880] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 20:14:06,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 20:14:06,880] [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
Croceibacter atlanticus	strain=HTCC2559	GCA_000196315.1	313588	313588	type	True	98.2363	887	934	95	conclusive
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.2922	142	934	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.2922	142	934	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	77.1101	89	934	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.9752	117	934	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.9668	90	934	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.9604	117	934	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.9417	83	934	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.9376	181	934	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	76.9044	86	934	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.8103	54	934	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.8083	130	934	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.6919	131	934	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.6912	133	934	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.6538	125	934	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.6378	138	934	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.63	118	934	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.5738	99	934	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.4441	86	934	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.3963	106	934	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.2755	137	934	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	76.1634	146	934	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	75.7766	68	934	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:06,880] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6696/tc_result.tsv
[2023-03-18 20:14:06,880] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:06,881] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:06,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/checkm_data
[2023-03-18 20:14:06,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:06,886] [INFO] Task started: CheckM
[2023-03-18 20:14:06,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6696/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6696/checkm_input OceanDNA-b6696/checkm_result
[2023-03-18 20:14:51,185] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:51,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:51,188] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:51,188] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:51,188] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6696/markers.fasta)
[2023-03-18 20:14:51,188] [INFO] Task started: Blastn
[2023-03-18 20:14:51,188] [INFO] Running command: blastn -query OceanDNA-b6696/markers.fasta -db /var/lib/cwl/stg3d20405c-bd2c-463e-8f7d-ef15ce24aa61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6696/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:52,243] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:52,243] [INFO] Selected 27 target genomes.
[2023-03-18 20:14:52,243] [INFO] Target genome list was writen to OceanDNA-b6696/target_genomes_gtdb.txt
[2023-03-18 20:14:52,555] [INFO] Task started: fastANI
[2023-03-18 20:14:52,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg29fd1980-b778-464e-a484-56c0c3e6f304/OceanDNA-b6696.fa --refList OceanDNA-b6696/target_genomes_gtdb.txt --output OceanDNA-b6696/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:08,042] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:08,056] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:08,057] [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_000196315.1	s__Croceibacter atlanticus	98.2363	887	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceibacter	95.0	98.48	98.33	0.94	0.89	6	conclusive
GCF_003095655.1	s__Dokdonia sp003095655	77.6713	97	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	77.296	141	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.1694	95	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	77.1414	88	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	77.093	130	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	76.9752	117	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_013249065.1	s__Winogradskyella litoriviva	76.9604	117	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.952	135	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	76.9488	150	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_900141885.1	s__Mesonia phycicola	76.9468	182	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.9398	87	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.9062	129	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	76.8994	130	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_013285155.1	s__Winogradskyella undariae	76.8304	146	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.00	96.07	0.88	0.85	4	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.8083	130	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	76.7853	117	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.7738	107	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.6912	133	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869935.1	s__Winogradskyella algicola	76.6538	125	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861125.1	s__Cellulophaga baltica_A	76.6377	94	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.6318	119	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.4736	133	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	76.4441	86	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCA_012964435.1	s__Mesonia sp012964435	76.3832	102	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCA_013139515.1	s__Lutibacter sp013139515	76.1499	58	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.0069	83	934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:08,057] [INFO] GTDB search result was written to OceanDNA-b6696/result_gtdb.tsv
[2023-03-18 20:15:08,057] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:08,059] [INFO] DFAST_QC result json was written to OceanDNA-b6696/dqc_result.json
[2023-03-18 20:15:08,060] [INFO] DFAST_QC completed!
[2023-03-18 20:15:08,060] [INFO] Total running time: 0h1m36s