[2023-03-19 04:55:39,419] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,420] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stg9bfb4c22-1b64-46a8-aaf3-d2b830bbb142/OceanDNA-b24685.fa | prodigal -d OceanDNA-b24685/cds.fna -a OceanDNA-b24685/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:56:01,632] [INFO] Task succeeded: Prodigal
[2023-03-19 04:56:01,632] [INFO] Task started: HMMsearch
[2023-03-19 04:56:01,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b24685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/reference_markers.hmm OceanDNA-b24685/protein.faa > /dev/null
[2023-03-19 04:56:01,831] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:56:01,831] [INFO] Found 6/6 markers.
[2023-03-19 04:56:01,854] [INFO] Query marker FASTA was written to OceanDNA-b24685/markers.fasta
[2023-03-19 04:56:01,855] [INFO] Task started: Blastn
[2023-03-19 04:56:01,855] [INFO] Running command: blastn -query OceanDNA-b24685/markers.fasta -db /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/reference_markers.fasta -out OceanDNA-b24685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:02,545] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:02,768] [INFO] Selected 33 target genomes.
[2023-03-19 04:56:02,768] [INFO] Target genome list was writen to OceanDNA-b24685/target_genomes.txt
[2023-03-19 04:56:02,793] [INFO] Task started: fastANI
[2023-03-19 04:56:02,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bfb4c22-1b64-46a8-aaf3-d2b830bbb142/OceanDNA-b24685.fa --refList OceanDNA-b24685/target_genomes.txt --output OceanDNA-b24685/fastani_result.tsv --threads 1
[2023-03-19 04:56:28,340] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:28,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:56:28,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:56:28,357] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:56:28,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:56:28,357] [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
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.6915	56	1106	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.6344	57	1106	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	76.8173	56	1106	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.5493	91	1106	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.5197	76	1106	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.2559	105	1106	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.0153	93	1106	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.9787	90	1106	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	75.9695	61	1106	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.9344	84	1106	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	75.9308	57	1106	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	75.9202	56	1106	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.9185	91	1106	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.9055	87	1106	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	75.8909	57	1106	95	below_threshold
Niveispirillum irakense	strain=DSM 11586	GCA_000429645.1	34011	34011	type	True	75.8853	93	1106	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.8809	95	1106	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	75.8422	58	1106	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	75.8343	100	1106	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.8022	99	1106	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.7907	116	1106	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	75.7803	123	1106	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	75.7748	59	1106	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.7206	119	1106	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6947	109	1106	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.5662	102	1106	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	75.4632	55	1106	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	75.4436	60	1106	95	below_threshold
Tepidamorphus gemmatus	strain=DSM 19345	GCA_004346195.1	747076	747076	type	True	75.2902	54	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:56:28,358] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24685/tc_result.tsv
[2023-03-19 04:56:28,361] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:56:28,361] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:56:28,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/checkm_data
[2023-03-19 04:56:28,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:56:28,369] [INFO] Task started: CheckM
[2023-03-19 04:56:28,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24685/checkm_input OceanDNA-b24685/checkm_result
[2023-03-19 04:57:22,102] [INFO] Task succeeded: CheckM
[2023-03-19 04:57:22,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:57:22,127] [INFO] ===== Completeness check finished =====
[2023-03-19 04:57:22,127] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:57:22,127] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24685/markers.fasta)
[2023-03-19 04:57:22,128] [INFO] Task started: Blastn
[2023-03-19 04:57:22,128] [INFO] Running command: blastn -query OceanDNA-b24685/markers.fasta -db /var/lib/cwl/stg3621a875-3d01-4248-92ef-9782373a9ce9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:57:23,355] [INFO] Task succeeded: Blastn
[2023-03-19 04:57:23,356] [INFO] Selected 27 target genomes.
[2023-03-19 04:57:23,356] [INFO] Target genome list was writen to OceanDNA-b24685/target_genomes_gtdb.txt
[2023-03-19 04:57:23,383] [INFO] Task started: fastANI
[2023-03-19 04:57:23,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bfb4c22-1b64-46a8-aaf3-d2b830bbb142/OceanDNA-b24685.fa --refList OceanDNA-b24685/target_genomes_gtdb.txt --output OceanDNA-b24685/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:57:44,526] [INFO] Task succeeded: fastANI
[2023-03-19 04:57:44,540] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:57:44,540] [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_002168225.1	s__TMED2 sp002168225	99.983	1092	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED2;f__TMED2;g__TMED2	95.0	99.94	99.84	0.98	0.96	15	conclusive
GCF_000739695.1	s__Tepidicaulis marinus	78.8209	56	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis	95.0	98.55	98.55	0.94	0.94	2	-
GCA_019192455.1	s__TMED2 sp019192455	77.1509	280	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED2;f__TMED2;g__TMED2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	76.8173	56	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.5493	91	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.2251	98	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	76.0002	89	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	75.9787	90	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003568845.1	s__Indioceanicola profundi	75.9719	87	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Indioceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000936425.1	s__Skermanella aerolata	75.9344	84	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.9055	87	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868735.1	s__Niveispirillum cyanobacteriorum	75.8343	100	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003336875.1	s__Oleisolibacter albus	75.8003	106	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	75.7899	124	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.7842	76	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	75.7538	102	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.7517	67	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	75.7311	127	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000702305.1	s__GCF-000702305 sp000702305	75.6606	67	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	75.6012	66	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	75.5867	122	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_900184795.1	s__Phaeospirillum sp900184795	75.5721	64	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	75.5552	116	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.4888	76	1106	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:57:44,540] [INFO] GTDB search result was written to OceanDNA-b24685/result_gtdb.tsv
[2023-03-19 04:57:44,540] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:57:44,543] [INFO] DFAST_QC result json was written to OceanDNA-b24685/dqc_result.json
[2023-03-19 04:57:44,543] [INFO] DFAST_QC completed!
[2023-03-19 04:57:44,543] [INFO] Total running time: 0h2m5s