[2023-03-14 12:25:41,513] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference
[2023-03-14 12:25:42,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,640] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,640] [INFO] Running command: cat /var/lib/cwl/stg5cbddd07-3024-4ee6-8757-c144a599c59f/OceanDNA-b34241.fa | prodigal -d OceanDNA-b34241/cds.fna -a OceanDNA-b34241/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:58,166] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:58,166] [INFO] Task started: HMMsearch
[2023-03-14 12:25:58,166] [INFO] Running command: hmmsearch --tblout OceanDNA-b34241/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/reference_markers.hmm OceanDNA-b34241/protein.faa > /dev/null
[2023-03-14 12:25:58,354] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:58,355] [INFO] Found 6/6 markers.
[2023-03-14 12:25:58,371] [INFO] Query marker FASTA was written to OceanDNA-b34241/markers.fasta
[2023-03-14 12:25:58,373] [INFO] Task started: Blastn
[2023-03-14 12:25:58,373] [INFO] Running command: blastn -query OceanDNA-b34241/markers.fasta -db /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/reference_markers.fasta -out OceanDNA-b34241/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:59,152] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:59,152] [INFO] Selected 32 target genomes.
[2023-03-14 12:25:59,153] [INFO] Target genome list was writen to OceanDNA-b34241/target_genomes.txt
[2023-03-14 12:25:59,175] [INFO] Task started: fastANI
[2023-03-14 12:25:59,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbddd07-3024-4ee6-8757-c144a599c59f/OceanDNA-b34241.fa --refList OceanDNA-b34241/target_genomes.txt --output OceanDNA-b34241/fastani_result.tsv --threads 1
[2023-03-14 12:26:18,214] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:18,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:18,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:18,230] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:18,230] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:18,230] [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
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.0115	130	810	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.9916	131	810	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.9747	130	810	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.9213	135	810	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.856	113	810	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.8265	108	810	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.7191	108	810	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	76.6995	95	810	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.691	74	810	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.631	104	810	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.6128	73	810	95	below_threshold
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	76.6075	84	810	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.3627	82	810	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.3135	63	810	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.2944	87	810	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	76.2842	67	810	95	below_threshold
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	76.2345	103	810	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.23	65	810	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.1022	67	810	95	below_threshold
Wenzhouxiangella marina	strain=KCTC 42284	GCA_001187785.1	1579979	1579979	type	True	76.045	50	810	95	below_threshold
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	76.0119	51	810	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.9282	76	810	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.9203	92	810	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.9061	77	810	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.8896	78	810	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.8583	87	810	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	75.4369	54	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:18,230] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34241/tc_result.tsv
[2023-03-14 12:26:18,230] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:18,230] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:18,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/checkm_data
[2023-03-14 12:26:18,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:18,236] [INFO] Task started: CheckM
[2023-03-14 12:26:18,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34241/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34241/checkm_input OceanDNA-b34241/checkm_result
[2023-03-14 12:26:59,514] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:59,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:59,517] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:59,517] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:59,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34241/markers.fasta)
[2023-03-14 12:26:59,518] [INFO] Task started: Blastn
[2023-03-14 12:26:59,518] [INFO] Running command: blastn -query OceanDNA-b34241/markers.fasta -db /var/lib/cwl/stg22c1c714-6421-4178-8d49-b3e00e183716/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34241/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:00,937] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:00,938] [INFO] Selected 26 target genomes.
[2023-03-14 12:27:00,938] [INFO] Target genome list was writen to OceanDNA-b34241/target_genomes_gtdb.txt
[2023-03-14 12:27:00,959] [INFO] Task started: fastANI
[2023-03-14 12:27:00,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbddd07-3024-4ee6-8757-c144a599c59f/OceanDNA-b34241.fa --refList OceanDNA-b34241/target_genomes_gtdb.txt --output OceanDNA-b34241/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:14,949] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:14,961] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:14,961] [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_000801295.1	s__MONJU sp000801295	78.2239	270	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020805.1	s__GCF-002020805 sp002020805	77.3946	90	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__GCF-002020805	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002009425.1	s__41T-STBD-0c-01a sp002009425	77.3781	185	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__41T-STBD-0c-01a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.2084	125	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696905.1	s__MONJU sp003696905	77.2078	178	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.0927	140	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	77.0355	133	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCA_003972985.1	s__Thiolapillus sp003972985	77.0181	126	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCA_009497875.2	s__JADGBD01 sp009497875	76.9803	134	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	76.9747	130	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224005.2	s__Marichromatium purpuratum	76.9213	135	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653295.1	s__Halochromatium salexigens	76.8366	89	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.7332	83	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_018812525.1	s__YD12-FULL-61-37 sp018812525	76.6919	103	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__YD12-FULL-61-37	95.0	99.98	99.98	0.97	0.97	3	-
GCA_011390365.1	s__SLIM01 sp011390365	76.6435	104	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	76.5661	61	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	-
GCA_011051655.1	s__DRKS01 sp011051655	76.5441	117	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583835.1	s__Thiococcus pfennigii	76.2999	99	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_009295635.1	s__S0819 sp009295635	76.2598	74	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	76.2277	57	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	75.7968	62	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:14,961] [INFO] GTDB search result was written to OceanDNA-b34241/result_gtdb.tsv
[2023-03-14 12:27:14,961] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:14,964] [INFO] DFAST_QC result json was written to OceanDNA-b34241/dqc_result.json
[2023-03-14 12:27:14,964] [INFO] DFAST_QC completed!
[2023-03-14 12:27:14,964] [INFO] Total running time: 0h1m33s