[2023-03-15 20:34:26,717] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,717] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference
[2023-03-15 20:34:28,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,458] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,458] [INFO] Running command: cat /var/lib/cwl/stgdaa41a67-6191-49d0-bfa3-260e3fe931d3/OceanDNA-b31421.fa | prodigal -d OceanDNA-b31421/cds.fna -a OceanDNA-b31421/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:54,054] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:54,054] [INFO] Task started: HMMsearch
[2023-03-15 20:34:54,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b31421/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/reference_markers.hmm OceanDNA-b31421/protein.faa > /dev/null
[2023-03-15 20:34:54,269] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:54,270] [INFO] Found 6/6 markers.
[2023-03-15 20:34:54,297] [INFO] Query marker FASTA was written to OceanDNA-b31421/markers.fasta
[2023-03-15 20:34:54,298] [INFO] Task started: Blastn
[2023-03-15 20:34:54,298] [INFO] Running command: blastn -query OceanDNA-b31421/markers.fasta -db /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/reference_markers.fasta -out OceanDNA-b31421/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:55,011] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:55,012] [INFO] Selected 35 target genomes.
[2023-03-15 20:34:55,012] [INFO] Target genome list was writen to OceanDNA-b31421/target_genomes.txt
[2023-03-15 20:34:55,033] [INFO] Task started: fastANI
[2023-03-15 20:34:55,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaa41a67-6191-49d0-bfa3-260e3fe931d3/OceanDNA-b31421.fa --refList OceanDNA-b31421/target_genomes.txt --output OceanDNA-b31421/fastani_result.tsv --threads 1
[2023-03-15 20:35:28,986] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:28,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:28,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:29,005] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:29,005] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:35:29,005] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.2113	294	1386	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.8947	450	1386	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.8746	341	1386	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.8145	452	1386	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.7502	316	1386	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.644	288	1386	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.5273	237	1386	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.5126	213	1386	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4342	253	1386	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.4231	294	1386	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.412	328	1386	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.4096	245	1386	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4078	288	1386	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.3916	282	1386	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.389	230	1386	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	76.3812	211	1386	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.3748	286	1386	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3469	334	1386	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.3327	299	1386	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.3224	313	1386	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.2987	252	1386	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.2674	238	1386	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.2213	200	1386	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.212	305	1386	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.1583	281	1386	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.0812	191	1386	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	75.9427	185	1386	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	75.9353	250	1386	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.7411	157	1386	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	75.7057	187	1386	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	75.7036	218	1386	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.5705	122	1386	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	75.4659	139	1386	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.3432	138	1386	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	75.1786	113	1386	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:35:29,267] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31421/tc_result.tsv
[2023-03-15 20:35:29,268] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:29,268] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:29,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/checkm_data
[2023-03-15 20:35:29,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:29,315] [INFO] Task started: CheckM
[2023-03-15 20:35:29,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31421/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31421/checkm_input OceanDNA-b31421/checkm_result
[2023-03-15 20:36:51,664] [INFO] Task succeeded: CheckM
[2023-03-15 20:36:51,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:36:51,667] [INFO] ===== Completeness check finished =====
[2023-03-15 20:36:51,668] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:36:51,668] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31421/markers.fasta)
[2023-03-15 20:36:51,668] [INFO] Task started: Blastn
[2023-03-15 20:36:51,668] [INFO] Running command: blastn -query OceanDNA-b31421/markers.fasta -db /var/lib/cwl/stg76acabd7-20e3-4a6a-9956-7a7bbf8c0f5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31421/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:36:52,927] [INFO] Task succeeded: Blastn
[2023-03-15 20:36:52,928] [INFO] Selected 29 target genomes.
[2023-03-15 20:36:52,928] [INFO] Target genome list was writen to OceanDNA-b31421/target_genomes_gtdb.txt
[2023-03-15 20:36:53,867] [INFO] Task started: fastANI
[2023-03-15 20:36:53,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgdaa41a67-6191-49d0-bfa3-260e3fe931d3/OceanDNA-b31421.fa --refList OceanDNA-b31421/target_genomes_gtdb.txt --output OceanDNA-b31421/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:37:19,009] [INFO] Task succeeded: fastANI
[2023-03-15 20:37:19,024] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:37:19,025] [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_014323865.1	s__SP197 sp014323865	78.7335	398	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722885.1	s__SP197 sp002722885	78.1454	458	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700655.1	s__SP197 sp018700655	77.8151	436	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SP197	95.0	99.23	99.15	0.84	0.82	5	-
GCF_014925385.1	s__WHTV01 sp014925385	77.2203	291	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869675.1	s__VGDP01 sp016869675	77.1318	317	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__VGDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.848	342	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.7127	319	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772935.1	s__Reyranella sp009772935	76.5393	214	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290035.1	s__Reyranella sp013290035	76.4886	169	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	76.4463	231	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_016765655.1	s__Skermanella mucosa	76.4392	287	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.4298	319	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	76.401	295	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	76.3977	229	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_001639105.2	s__Azospirillum humicireducens	76.397	255	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	76.3773	283	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792585.1	s__SHVZ01 sp016792585	76.369	244	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	76.2732	264	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.2555	285	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.2424	301	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.2369	309	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.2211	335	1386	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_016870055.1	s__Reyranella sp016870055	76.1842	214	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	76.1774	181	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364825.1	s__Azospirillum sp008364825	76.0898	299	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCA_902826935.1	s__CADEGR01 sp902826935	76.0409	237	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCF_014193375.1	s__Halomonas campaniensis	75.4535	138	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	75.3368	139	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487895.1	s__S144-34 sp015487895	75.186	80	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:37:19,025] [INFO] GTDB search result was written to OceanDNA-b31421/result_gtdb.tsv
[2023-03-15 20:37:19,025] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:37:19,028] [INFO] DFAST_QC result json was written to OceanDNA-b31421/dqc_result.json
[2023-03-15 20:37:19,028] [INFO] DFAST_QC completed!
[2023-03-15 20:37:19,028] [INFO] Total running time: 0h2m52s