[2023-03-15 21:24:36,548] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,549] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference
[2023-03-15 21:24:37,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,656] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,656] [INFO] Running command: cat /var/lib/cwl/stga0457470-84f3-4b85-a315-1f18391b9970/OceanDNA-b36140.fa | prodigal -d OceanDNA-b36140/cds.fna -a OceanDNA-b36140/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:56,772] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:56,773] [INFO] Task started: HMMsearch
[2023-03-15 21:24:56,773] [INFO] Running command: hmmsearch --tblout OceanDNA-b36140/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/reference_markers.hmm OceanDNA-b36140/protein.faa > /dev/null
[2023-03-15 21:24:56,971] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:56,971] [INFO] Found 6/6 markers.
[2023-03-15 21:24:56,993] [INFO] Query marker FASTA was written to OceanDNA-b36140/markers.fasta
[2023-03-15 21:24:56,994] [INFO] Task started: Blastn
[2023-03-15 21:24:56,994] [INFO] Running command: blastn -query OceanDNA-b36140/markers.fasta -db /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/reference_markers.fasta -out OceanDNA-b36140/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:57,809] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:57,810] [INFO] Selected 33 target genomes.
[2023-03-15 21:24:57,811] [INFO] Target genome list was writen to OceanDNA-b36140/target_genomes.txt
[2023-03-15 21:24:57,825] [INFO] Task started: fastANI
[2023-03-15 21:24:57,826] [INFO] Running command: fastANI --query /var/lib/cwl/stga0457470-84f3-4b85-a315-1f18391b9970/OceanDNA-b36140.fa --refList OceanDNA-b36140/target_genomes.txt --output OceanDNA-b36140/fastani_result.tsv --threads 1
[2023-03-15 21:25:18,712] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:18,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:18,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:18,729] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:18,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:25:18,730] [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
Abyssibacter profundi	strain=OUC007	GCA_003151135.1	2182787	2182787	type	True	79.5249	470	1020	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	76.5289	173	1020	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.4992	75	1020	95	below_threshold
Oceanococcus atlanticus	strain=22II-S10r2	GCA_002088235.1	1317117	1317117	type	True	76.4827	104	1020	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	76.4681	120	1020	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.4562	191	1020	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.4513	122	1020	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.4414	193	1020	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	76.3585	188	1020	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.3541	83	1020	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	76.2981	92	1020	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.2931	109	1020	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	76.2906	132	1020	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2732	137	1020	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	76.2707	166	1020	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.2583	89	1020	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.1759	99	1020	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.145	112	1020	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.1413	140	1020	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.1068	71	1020	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.0993	140	1020	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	76.0915	146	1020	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.0761	143	1020	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.0598	146	1020	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	76.0597	117	1020	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	75.9911	91	1020	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.9706	123	1020	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.9361	83	1020	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	75.8523	64	1020	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	75.8223	77	1020	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.6741	100	1020	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	75.6494	82	1020	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	75.3357	69	1020	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:18,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36140/tc_result.tsv
[2023-03-15 21:25:18,730] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:18,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:18,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/checkm_data
[2023-03-15 21:25:18,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:18,795] [INFO] Task started: CheckM
[2023-03-15 21:25:18,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36140/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36140/checkm_input OceanDNA-b36140/checkm_result
[2023-03-15 21:26:08,492] [INFO] Task succeeded: CheckM
[2023-03-15 21:26:08,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:26:08,495] [INFO] ===== Completeness check finished =====
[2023-03-15 21:26:08,495] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:26:08,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36140/markers.fasta)
[2023-03-15 21:26:08,496] [INFO] Task started: Blastn
[2023-03-15 21:26:08,496] [INFO] Running command: blastn -query OceanDNA-b36140/markers.fasta -db /var/lib/cwl/stg7654b3b5-8a7a-45fd-8d48-259d28cd7ce8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36140/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:26:09,970] [INFO] Task succeeded: Blastn
[2023-03-15 21:26:09,971] [INFO] Selected 31 target genomes.
[2023-03-15 21:26:09,971] [INFO] Target genome list was writen to OceanDNA-b36140/target_genomes_gtdb.txt
[2023-03-15 21:26:10,280] [INFO] Task started: fastANI
[2023-03-15 21:26:10,280] [INFO] Running command: fastANI --query /var/lib/cwl/stga0457470-84f3-4b85-a315-1f18391b9970/OceanDNA-b36140.fa --refList OceanDNA-b36140/target_genomes_gtdb.txt --output OceanDNA-b36140/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:26:27,607] [INFO] Task succeeded: fastANI
[2023-03-15 21:26:27,625] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:26:27,626] [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_003151135.1	s__Abyssibacter profundi	79.5287	470	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__Abyssibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCA_018222345.1	s__JAAFAL01 sp018222345	77.1728	162	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__JAAFAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	76.7308	74	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.7087	99	1020	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	-
GCF_000378305.1	s__Thioalkalivibrio sp000378305	76.6499	73	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	98.92	98.55	0.95	0.94	12	-
GCA_016779605.1	s__Nevskia sp016779605	76.514	159	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088235.1	s__Oceanococcus atlanticus	76.5033	103	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Oceanococcaceae;g__Oceanococcus	95.0	98.37	98.37	0.93	0.93	2	-
GCF_000381825.1	s__Thioalkalivibrio sp000381825	76.5005	61	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.5002	65	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385215.1	s__Thioalkalivibrio thiocyanoxidans	76.4992	75	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.32	98.64	0.97	0.95	3	-
GCF_003788635.1	s__Salinisphaera orenii	76.4686	121	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	76.4509	121	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	76.4414	193	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000377405.1	s__Thioalkalivibrio sp000377405	76.362	88	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCF_900112865.1	s__Dyella marensis	76.2983	110	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003024235.1	s__Arenimonas caeni	76.2712	108	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381945.1	s__Thioalkalivibrio sp000381945	76.248	85	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	76.241	118	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_012272825.1	s__GCA-2722315 sp012272825	76.2271	100	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	76.1912	98	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112375.1	s__Pseudomonas citronellolis	76.1289	141	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCA_002699185.1	s__Thiohalobacter sp002699185	76.0893	78	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	76.0654	144	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCA_003252455.1	s__SZUA-467 sp003252455	76.0064	76	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SZUA-467	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212015.1	s__28-57-27 sp006212015	75.9555	51	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731955.1	s__Halomonas_C zincidurans	75.933	73	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178375.1	s__Ch67 sp013178375	75.9241	59	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435595.1	s__Stenotrophomonas maltophilia_AC	75.8743	91	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.01	98.85	0.95	0.92	3	-
GCF_003788585.1	s__Salinisphaera japonica	75.8523	64	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	75.846	82	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002699145.1	s__Halioglobus sp002699145	75.4464	84	1020	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:26:27,626] [INFO] GTDB search result was written to OceanDNA-b36140/result_gtdb.tsv
[2023-03-15 21:26:27,626] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:26:27,629] [INFO] DFAST_QC result json was written to OceanDNA-b36140/dqc_result.json
[2023-03-15 21:26:27,629] [INFO] DFAST_QC completed!
[2023-03-15 21:26:27,629] [INFO] Total running time: 0h1m51s