[2023-03-19 03:10:00,784] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,784] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference
[2023-03-19 03:10:01,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,893] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,894] [INFO] Running command: cat /var/lib/cwl/stgce275dc3-99ec-4766-8795-a33b85d18738/OceanDNA-b32943.fa | prodigal -d OceanDNA-b32943/cds.fna -a OceanDNA-b32943/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:21,771] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:21,772] [INFO] Task started: HMMsearch
[2023-03-19 03:10:21,772] [INFO] Running command: hmmsearch --tblout OceanDNA-b32943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/reference_markers.hmm OceanDNA-b32943/protein.faa > /dev/null
[2023-03-19 03:10:21,970] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:21,971] [INFO] Found 6/6 markers.
[2023-03-19 03:10:21,994] [INFO] Query marker FASTA was written to OceanDNA-b32943/markers.fasta
[2023-03-19 03:10:21,994] [INFO] Task started: Blastn
[2023-03-19 03:10:21,994] [INFO] Running command: blastn -query OceanDNA-b32943/markers.fasta -db /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/reference_markers.fasta -out OceanDNA-b32943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:22,776] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:22,777] [INFO] Selected 30 target genomes.
[2023-03-19 03:10:22,777] [INFO] Target genome list was writen to OceanDNA-b32943/target_genomes.txt
[2023-03-19 03:10:22,789] [INFO] Task started: fastANI
[2023-03-19 03:10:22,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgce275dc3-99ec-4766-8795-a33b85d18738/OceanDNA-b32943.fa --refList OceanDNA-b32943/target_genomes.txt --output OceanDNA-b32943/fastani_result.tsv --threads 1
[2023-03-19 03:10:46,857] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:46,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:46,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:46,873] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:46,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:10:46,873] [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
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.5696	124	1074	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3047	150	1074	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.2818	145	1074	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.2664	177	1074	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1589	133	1074	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.1439	115	1074	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0984	142	1074	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.0943	195	1074	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0097	124	1074	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.9127	119	1074	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.8834	182	1074	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.883	152	1074	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.8288	68	1074	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.8102	91	1074	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.7728	153	1074	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.7582	158	1074	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.7431	158	1074	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.7008	233	1074	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.6815	232	1074	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.6555	188	1074	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.6375	177	1074	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.5675	156	1074	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	75.4659	65	1074	95	below_threshold
Lichenibacterium minor	strain=RmlP026	GCA_004137685.1	2316528	2316528	type	True	75.3808	118	1074	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	75.3806	88	1074	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	75.3619	67	1074	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.357	170	1074	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	75.3009	75	1074	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.25	82	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:10:46,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32943/tc_result.tsv
[2023-03-19 03:10:46,873] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:46,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:46,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/checkm_data
[2023-03-19 03:10:46,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:46,879] [INFO] Task started: CheckM
[2023-03-19 03:10:46,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32943/checkm_input OceanDNA-b32943/checkm_result
[2023-03-19 03:11:36,878] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:36,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:36,881] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:36,881] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:36,881] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32943/markers.fasta)
[2023-03-19 03:11:36,882] [INFO] Task started: Blastn
[2023-03-19 03:11:36,882] [INFO] Running command: blastn -query OceanDNA-b32943/markers.fasta -db /var/lib/cwl/stg189b6261-467a-49e0-8178-fea99da313fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:38,375] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:38,376] [INFO] Selected 20 target genomes.
[2023-03-19 03:11:38,376] [INFO] Target genome list was writen to OceanDNA-b32943/target_genomes_gtdb.txt
[2023-03-19 03:11:38,496] [INFO] Task started: fastANI
[2023-03-19 03:11:38,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgce275dc3-99ec-4766-8795-a33b85d18738/OceanDNA-b32943.fa --refList OceanDNA-b32943/target_genomes_gtdb.txt --output OceanDNA-b32943/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:54,773] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:54,784] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:11:54,784] [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_002937555.1	s__PTKB01 sp002937555	83.6229	491	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	81.6831	702	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_011523425.1	s__WTGU01 sp011523425	77.3868	281	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717225.1	s__PTKB01 sp002717225	76.5263	181	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.3047	150	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.2818	145	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.2305	242	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.184	144	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.1571	151	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.1255	136	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.1106	141	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.1056	194	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	75.9769	142	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008364795.1	s__Azospirillum oryzae	75.8722	153	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCA_006738865.1	s__Stella sp006738865	75.8578	178	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	75.8289	176	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.6828	232	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017876095.1	s__Azospirillum agricola	75.6235	179	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.5187	117	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_003116095.1	s__Azospirillum sp003116095	75.5084	186	1074	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:54,785] [INFO] GTDB search result was written to OceanDNA-b32943/result_gtdb.tsv
[2023-03-19 03:11:54,785] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:54,787] [INFO] DFAST_QC result json was written to OceanDNA-b32943/dqc_result.json
[2023-03-19 03:11:54,787] [INFO] DFAST_QC completed!
[2023-03-19 03:11:54,787] [INFO] Total running time: 0h1m54s