[2023-03-18 21:23:39,778] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:23:39,778] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:23:39,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference
[2023-03-18 21:23:44,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:23:44,496] [INFO] Task started: Prodigal
[2023-03-18 21:23:44,496] [INFO] Running command: cat /var/lib/cwl/stg4cef885c-2d09-454f-acf2-709a3116a58f/OceanDNA-b30487.fa | prodigal -d OceanDNA-b30487/cds.fna -a OceanDNA-b30487/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:24:07,503] [INFO] Task succeeded: Prodigal
[2023-03-18 21:24:07,503] [INFO] Task started: HMMsearch
[2023-03-18 21:24:07,503] [INFO] Running command: hmmsearch --tblout OceanDNA-b30487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/reference_markers.hmm OceanDNA-b30487/protein.faa > /dev/null
[2023-03-18 21:24:07,777] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:24:07,778] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4cef885c-2d09-454f-acf2-709a3116a58f/OceanDNA-b30487.fa]
[2023-03-18 21:24:07,801] [INFO] Query marker FASTA was written to OceanDNA-b30487/markers.fasta
[2023-03-18 21:24:07,802] [INFO] Task started: Blastn
[2023-03-18 21:24:07,802] [INFO] Running command: blastn -query OceanDNA-b30487/markers.fasta -db /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/reference_markers.fasta -out OceanDNA-b30487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:24:11,026] [INFO] Task succeeded: Blastn
[2023-03-18 21:24:11,027] [INFO] Selected 21 target genomes.
[2023-03-18 21:24:11,027] [INFO] Target genome list was writen to OceanDNA-b30487/target_genomes.txt
[2023-03-18 21:24:11,043] [INFO] Task started: fastANI
[2023-03-18 21:24:11,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cef885c-2d09-454f-acf2-709a3116a58f/OceanDNA-b30487.fa --refList OceanDNA-b30487/target_genomes.txt --output OceanDNA-b30487/fastani_result.tsv --threads 1
[2023-03-18 21:24:26,701] [INFO] Task succeeded: fastANI
[2023-03-18 21:24:26,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:24:26,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:24:26,798] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:24:26,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:24:26,798] [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
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.7672	520	1166	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.76	537	1166	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	78.4249	505	1166	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	78.3908	529	1166	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.3042	467	1166	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.0176	399	1166	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8955	393	1166	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.8952	340	1166	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.8642	408	1166	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.6877	392	1166	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.6784	388	1166	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3058	317	1166	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.2948	345	1166	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.2004	290	1166	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.978	340	1166	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.9704	347	1166	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.9506	233	1166	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8004	242	1166	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.7144	241	1166	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.6775	246	1166	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.3671	138	1166	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:24:26,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30487/tc_result.tsv
[2023-03-18 21:24:26,798] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:24:26,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:24:26,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/checkm_data
[2023-03-18 21:24:26,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:24:26,804] [INFO] Task started: CheckM
[2023-03-18 21:24:26,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30487/checkm_input OceanDNA-b30487/checkm_result
[2023-03-18 21:25:30,711] [INFO] Task succeeded: CheckM
[2023-03-18 21:25:30,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:25:30,714] [INFO] ===== Completeness check finished =====
[2023-03-18 21:25:30,714] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:25:30,714] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30487/markers.fasta)
[2023-03-18 21:25:30,716] [INFO] Task started: Blastn
[2023-03-18 21:25:30,716] [INFO] Running command: blastn -query OceanDNA-b30487/markers.fasta -db /var/lib/cwl/stg10593688-e328-41d8-bff0-bddbd89b22a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:25:32,936] [INFO] Task succeeded: Blastn
[2023-03-18 21:25:32,937] [INFO] Selected 13 target genomes.
[2023-03-18 21:25:32,937] [INFO] Target genome list was writen to OceanDNA-b30487/target_genomes_gtdb.txt
[2023-03-18 21:25:32,949] [INFO] Task started: fastANI
[2023-03-18 21:25:32,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cef885c-2d09-454f-acf2-709a3116a58f/OceanDNA-b30487.fa --refList OceanDNA-b30487/target_genomes_gtdb.txt --output OceanDNA-b30487/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:25:43,166] [INFO] Task succeeded: fastANI
[2023-03-18 21:25:43,174] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:25:43,174] [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_900143535.1	s__Tateyamaria sp900143535	79.9868	701	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	79.6405	644	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	79.2033	615	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	79.0522	610	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651375.1	s__Tateyamaria omphalii	78.376	531	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.3264	463	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	78.0222	424	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_015644665.1	s__Roseobacter sp015644665	77.9564	443	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634885.1	s__Sulfitobacter sp001634885	77.8641	347	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_005434965.1	s__Marimonas lutisalis	77.5353	361	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.0005	343	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900112755.1	s__Sulfitobacter brevis	76.9416	293	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.7144	241	1166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:25:43,175] [INFO] GTDB search result was written to OceanDNA-b30487/result_gtdb.tsv
[2023-03-18 21:25:43,175] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:25:43,176] [INFO] DFAST_QC result json was written to OceanDNA-b30487/dqc_result.json
[2023-03-18 21:25:43,177] [INFO] DFAST_QC completed!
[2023-03-18 21:25:43,177] [INFO] Total running time: 0h2m3s