[2023-03-16 00:09:30,331] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:09:30,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:09:30,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference
[2023-03-16 00:09:32,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:09:32,556] [INFO] Task started: Prodigal
[2023-03-16 00:09:32,556] [INFO] Running command: cat /var/lib/cwl/stg6672a89e-a9ee-4110-b547-427ef982aecf/OceanDNA-b32689.fa | prodigal -d OceanDNA-b32689/cds.fna -a OceanDNA-b32689/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:09:52,856] [INFO] Task succeeded: Prodigal
[2023-03-16 00:09:52,856] [INFO] Task started: HMMsearch
[2023-03-16 00:09:52,856] [INFO] Running command: hmmsearch --tblout OceanDNA-b32689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/reference_markers.hmm OceanDNA-b32689/protein.faa > /dev/null
[2023-03-16 00:09:53,055] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:09:53,055] [INFO] Found 6/6 markers.
[2023-03-16 00:09:53,079] [INFO] Query marker FASTA was written to OceanDNA-b32689/markers.fasta
[2023-03-16 00:09:53,080] [INFO] Task started: Blastn
[2023-03-16 00:09:53,080] [INFO] Running command: blastn -query OceanDNA-b32689/markers.fasta -db /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/reference_markers.fasta -out OceanDNA-b32689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:09:53,859] [INFO] Task succeeded: Blastn
[2023-03-16 00:09:53,860] [INFO] Selected 37 target genomes.
[2023-03-16 00:09:53,861] [INFO] Target genome list was writen to OceanDNA-b32689/target_genomes.txt
[2023-03-16 00:09:53,882] [INFO] Task started: fastANI
[2023-03-16 00:09:53,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg6672a89e-a9ee-4110-b547-427ef982aecf/OceanDNA-b32689.fa --refList OceanDNA-b32689/target_genomes.txt --output OceanDNA-b32689/fastani_result.tsv --threads 1
[2023-03-16 00:10:24,299] [INFO] Task succeeded: fastANI
[2023-03-16 00:10:24,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:10:24,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:10:24,318] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:10:24,318] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:10:24,318] [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
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.2731	119	1053	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2188	151	1053	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.1651	141	1053	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.1233	120	1053	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	76.1064	53	1053	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.0791	144	1053	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.0607	190	1053	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.0444	112	1053	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.029	194	1053	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.0005	145	1053	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.9878	128	1053	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.987	113	1053	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.9781	150	1053	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.9728	150	1053	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.9153	170	1053	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8845	203	1053	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.8374	102	1053	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.7725	96	1053	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.6965	129	1053	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.683	89	1053	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	75.6663	119	1053	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.6613	99	1053	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	75.6361	64	1053	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	75.5969	92	1053	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.5877	103	1053	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.5676	122	1053	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.5395	162	1053	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.5293	128	1053	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	75.5099	72	1053	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	75.5097	51	1053	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	75.3703	88	1053	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.3633	144	1053	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.3317	57	1053	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	75.2002	69	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:10:24,319] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32689/tc_result.tsv
[2023-03-16 00:10:24,319] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:10:24,320] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:10:24,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/checkm_data
[2023-03-16 00:10:24,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:10:24,414] [INFO] Task started: CheckM
[2023-03-16 00:10:24,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32689/checkm_input OceanDNA-b32689/checkm_result
[2023-03-16 00:11:14,255] [INFO] Task succeeded: CheckM
[2023-03-16 00:11:14,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:11:14,258] [INFO] ===== Completeness check finished =====
[2023-03-16 00:11:14,259] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:11:14,259] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32689/markers.fasta)
[2023-03-16 00:11:14,260] [INFO] Task started: Blastn
[2023-03-16 00:11:14,260] [INFO] Running command: blastn -query OceanDNA-b32689/markers.fasta -db /var/lib/cwl/stg28745e2d-dd83-408a-9d0b-714a3700e801/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:11:15,857] [INFO] Task succeeded: Blastn
[2023-03-16 00:11:15,859] [INFO] Selected 31 target genomes.
[2023-03-16 00:11:15,859] [INFO] Target genome list was writen to OceanDNA-b32689/target_genomes_gtdb.txt
[2023-03-16 00:11:15,885] [INFO] Task started: fastANI
[2023-03-16 00:11:15,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg6672a89e-a9ee-4110-b547-427ef982aecf/OceanDNA-b32689.fa --refList OceanDNA-b32689/target_genomes_gtdb.txt --output OceanDNA-b32689/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:11:36,175] [INFO] Task succeeded: fastANI
[2023-03-16 00:11:36,189] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:11:36,189] [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_002690215.1	s__GCA-2690215 sp002690215	99.5044	897	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016869515.1	s__VGDZ01 sp016869515	76.5284	170	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869235.1	s__CAIVPW01 sp016869235	76.3929	80	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CAIVPW01;f__CAIVPW01;g__CAIVPW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	76.277	120	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.1129	144	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	76.0601	103	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCF_002924445.1	s__Minwuia thermotolerans	76.0459	147	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_009377375.1	s__WHUE01 sp009377375	76.0436	110	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	76.0205	67	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_016869415.1	s__VGEI01 sp016869415	75.9081	105	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	75.8763	106	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197755.1	s__Ferrovibrio terrae	75.8374	102	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	75.7967	127	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333275.1	s__Nitrospirillum sp000333275	75.7525	121	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	75.7525	140	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687515.1	s__GCA-2687515 sp002687515	75.744	102	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2687515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.7106	91	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	75.7073	136	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	75.6478	177	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	75.5719	88	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	75.5674	146	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCA_004356985.1	s__SMXQ01 sp004356985	75.5632	85	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	75.5411	129	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCA_004173095.1	s__Tardiphaga sp004173095	75.0492	54	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:11:36,190] [INFO] GTDB search result was written to OceanDNA-b32689/result_gtdb.tsv
[2023-03-16 00:11:36,190] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:11:36,194] [INFO] DFAST_QC result json was written to OceanDNA-b32689/dqc_result.json
[2023-03-16 00:11:36,195] [INFO] DFAST_QC completed!
[2023-03-16 00:11:36,195] [INFO] Total running time: 0h2m6s