[2023-03-17 03:29:19,762] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:29:19,763] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:29:19,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference
[2023-03-17 03:29:21,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:29:21,321] [INFO] Task started: Prodigal
[2023-03-17 03:29:21,322] [INFO] Running command: cat /var/lib/cwl/stgc9a3a273-ed8a-44e4-ad49-9cbf45d31def/OceanDNA-b29391.fa | prodigal -d OceanDNA-b29391/cds.fna -a OceanDNA-b29391/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:30,206] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:30,206] [INFO] Task started: HMMsearch
[2023-03-17 03:29:30,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b29391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/reference_markers.hmm OceanDNA-b29391/protein.faa > /dev/null
[2023-03-17 03:29:30,360] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:30,361] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc9a3a273-ed8a-44e4-ad49-9cbf45d31def/OceanDNA-b29391.fa]
[2023-03-17 03:29:30,376] [INFO] Query marker FASTA was written to OceanDNA-b29391/markers.fasta
[2023-03-17 03:29:30,376] [INFO] Task started: Blastn
[2023-03-17 03:29:30,376] [INFO] Running command: blastn -query OceanDNA-b29391/markers.fasta -db /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/reference_markers.fasta -out OceanDNA-b29391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:30,994] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:30,995] [INFO] Selected 23 target genomes.
[2023-03-17 03:29:30,995] [INFO] Target genome list was writen to OceanDNA-b29391/target_genomes.txt
[2023-03-17 03:29:31,006] [INFO] Task started: fastANI
[2023-03-17 03:29:31,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a3a273-ed8a-44e4-ad49-9cbf45d31def/OceanDNA-b29391.fa --refList OceanDNA-b29391/target_genomes.txt --output OceanDNA-b29391/fastani_result.tsv --threads 1
[2023-03-17 03:29:46,817] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:46,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:46,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:46,830] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:46,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:29:46,830] [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
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.7038	283	463	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.0943	229	463	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	77.7123	240	463	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	77.6984	241	463	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	77.5567	190	463	95	below_threshold
Jannaschia aquimarina	strain=GSW-M26	GCA_000877395.1	935700	935700	type	True	77.4949	193	463	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.1429	196	463	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.1391	194	463	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.0978	198	463	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.0819	149	463	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	77.0156	154	463	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.9719	155	463	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	76.8915	155	463	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	76.7093	177	463	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	76.7061	142	463	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	76.6395	182	463	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	76.6362	178	463	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.4934	121	463	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3816	113	463	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	76.3671	110	463	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.0757	162	463	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.0176	174	463	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.9739	147	463	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:46,830] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29391/tc_result.tsv
[2023-03-17 03:29:46,830] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:46,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:46,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/checkm_data
[2023-03-17 03:29:46,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:46,835] [INFO] Task started: CheckM
[2023-03-17 03:29:46,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29391/checkm_input OceanDNA-b29391/checkm_result
[2023-03-17 03:30:12,821] [INFO] Task succeeded: CheckM
[2023-03-17 03:30:12,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:30:12,823] [INFO] ===== Completeness check finished =====
[2023-03-17 03:30:12,824] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:30:12,824] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29391/markers.fasta)
[2023-03-17 03:30:12,824] [INFO] Task started: Blastn
[2023-03-17 03:30:12,824] [INFO] Running command: blastn -query OceanDNA-b29391/markers.fasta -db /var/lib/cwl/stg6d7560d3-e41c-41b8-862e-53525cc3ceaa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:30:13,823] [INFO] Task succeeded: Blastn
[2023-03-17 03:30:13,823] [INFO] Selected 19 target genomes.
[2023-03-17 03:30:13,824] [INFO] Target genome list was writen to OceanDNA-b29391/target_genomes_gtdb.txt
[2023-03-17 03:30:13,857] [INFO] Task started: fastANI
[2023-03-17 03:30:13,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9a3a273-ed8a-44e4-ad49-9cbf45d31def/OceanDNA-b29391.fa --refList OceanDNA-b29391/target_genomes_gtdb.txt --output OceanDNA-b29391/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:30:27,070] [INFO] Task succeeded: fastANI
[2023-03-17 03:30:27,080] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:30:27,081] [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_016820245.1	s__Jannaschia sp016820245	83.847	399	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.7192	282	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	78.0943	229	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.7671	187	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	77.6863	242	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001408515.1	s__Jannaschia seosinensis	77.4087	164	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	77.1779	192	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.0507	194	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	77.0216	188	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	77.0214	203	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.8079	119	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	76.6667	169	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	76.6597	166	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_003993775.1	s__Frigidibacter sp003993775	76.6548	147	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	76.6467	175	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	76.4173	136	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	76.3671	110	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551745.1	s__Rhodobaculum sp003551745	76.1291	95	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106695.1	s__Albimonas donghaensis	76.0456	171	463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-17 03:30:27,081] [INFO] GTDB search result was written to OceanDNA-b29391/result_gtdb.tsv
[2023-03-17 03:30:27,081] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:30:27,083] [INFO] DFAST_QC result json was written to OceanDNA-b29391/dqc_result.json
[2023-03-17 03:30:27,083] [INFO] DFAST_QC completed!
[2023-03-17 03:30:27,083] [INFO] Total running time: 0h1m7s