[2023-06-29 01:21:31,011] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:21:31,012] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:21:31,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference
[2023-06-29 01:21:32,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:21:32,230] [INFO] Task started: Prodigal
[2023-06-29 01:21:32,230] [INFO] Running command: gunzip -c /var/lib/cwl/stge06cba2f-91ec-4f63-8b7d-f47da0282dfc/GCA_020430745.1_ASM2043074v1_genomic.fna.gz | prodigal -d GCA_020430745.1_ASM2043074v1_genomic.fna/cds.fna -a GCA_020430745.1_ASM2043074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:22:23,983] [INFO] Task succeeded: Prodigal
[2023-06-29 01:22:23,983] [INFO] Task started: HMMsearch
[2023-06-29 01:22:23,983] [INFO] Running command: hmmsearch --tblout GCA_020430745.1_ASM2043074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/reference_markers.hmm GCA_020430745.1_ASM2043074v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:22:24,378] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:22:24,380] [INFO] Found 6/6 markers.
[2023-06-29 01:22:24,456] [INFO] Query marker FASTA was written to GCA_020430745.1_ASM2043074v1_genomic.fna/markers.fasta
[2023-06-29 01:22:24,456] [INFO] Task started: Blastn
[2023-06-29 01:22:24,456] [INFO] Running command: blastn -query GCA_020430745.1_ASM2043074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/reference_markers.fasta -out GCA_020430745.1_ASM2043074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:22:25,240] [INFO] Task succeeded: Blastn
[2023-06-29 01:22:25,245] [INFO] Selected 39 target genomes.
[2023-06-29 01:22:25,245] [INFO] Target genome list was writen to GCA_020430745.1_ASM2043074v1_genomic.fna/target_genomes.txt
[2023-06-29 01:22:25,249] [INFO] Task started: fastANI
[2023-06-29 01:22:25,249] [INFO] Running command: fastANI --query /var/lib/cwl/stge06cba2f-91ec-4f63-8b7d-f47da0282dfc/GCA_020430745.1_ASM2043074v1_genomic.fna.gz --refList GCA_020430745.1_ASM2043074v1_genomic.fna/target_genomes.txt --output GCA_020430745.1_ASM2043074v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:22:58,230] [INFO] Task succeeded: fastANI
[2023-06-29 01:22:58,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:22:58,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:22:58,261] [INFO] Found 36 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:22:58,261] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:22:58,262] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4145	196	2348	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1545	365	2348	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.1529	306	2348	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	75.1224	56	2348	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.1152	72	2348	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.1083	81	2348	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	75.0748	398	2348	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.0534	362	2348	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.0496	156	2348	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	75.0298	405	2348	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.0224	380	2348	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	75.0079	106	2348	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	74.9915	98	2348	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	74.9836	154	2348	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	74.9702	176	2348	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9612	214	2348	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	74.9531	68	2348	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	74.9229	93	2348	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	74.9141	80	2348	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.9106	418	2348	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.9078	227	2348	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	74.9044	68	2348	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	74.8946	112	2348	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.862	261	2348	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	74.8517	157	2348	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	74.845	127	2348	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	74.8346	154	2348	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	74.8292	153	2348	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	74.8058	92	2348	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	74.7996	121	2348	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	74.7927	141	2348	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	74.7871	143	2348	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	74.7791	102	2348	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	74.7753	104	2348	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	74.745	209	2348	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	74.7174	327	2348	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:22:58,264] [INFO] DFAST Taxonomy check result was written to GCA_020430745.1_ASM2043074v1_genomic.fna/tc_result.tsv
[2023-06-29 01:22:58,264] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:22:58,264] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:22:58,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/checkm_data
[2023-06-29 01:22:58,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:22:58,347] [INFO] Task started: CheckM
[2023-06-29 01:22:58,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020430745.1_ASM2043074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020430745.1_ASM2043074v1_genomic.fna/checkm_input GCA_020430745.1_ASM2043074v1_genomic.fna/checkm_result
[2023-06-29 01:24:38,976] [INFO] Task succeeded: CheckM
[2023-06-29 01:24:38,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.80%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:24:39,012] [INFO] ===== Completeness check finished =====
[2023-06-29 01:24:39,012] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:24:39,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020430745.1_ASM2043074v1_genomic.fna/markers.fasta)
[2023-06-29 01:24:39,013] [INFO] Task started: Blastn
[2023-06-29 01:24:39,013] [INFO] Running command: blastn -query GCA_020430745.1_ASM2043074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea518e8-f564-4bdc-b9d2-f1dc1f466eed/dqc_reference/reference_markers_gtdb.fasta -out GCA_020430745.1_ASM2043074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:24:40,284] [INFO] Task succeeded: Blastn
[2023-06-29 01:24:40,290] [INFO] Selected 40 target genomes.
[2023-06-29 01:24:40,290] [INFO] Target genome list was writen to GCA_020430745.1_ASM2043074v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:24:40,317] [INFO] Task started: fastANI
[2023-06-29 01:24:40,318] [INFO] Running command: fastANI --query /var/lib/cwl/stge06cba2f-91ec-4f63-8b7d-f47da0282dfc/GCA_020430745.1_ASM2043074v1_genomic.fna.gz --refList GCA_020430745.1_ASM2043074v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020430745.1_ASM2043074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:25:16,891] [INFO] Task succeeded: fastANI
[2023-06-29 01:25:16,922] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:25:16,922] [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_016703535.1	s__JADJBV01 sp016703535	76.4105	513	2348	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__JADJBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526105.1	s__WYAZ01 sp011526105	76.0225	274	2348	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__WYAZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242475.1	s__ZC4RG40 sp003242475	75.4041	104	2348	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874275.1	s__CAIOAK01 sp903874275	75.2709	228	2348	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.83	99.81	0.95	0.94	3	-
GCA_003695825.1	s__J048 sp003695825	75.2357	60	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191815.1	s__JACPVI01 sp016191815	75.2201	234	2348	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JACPVI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	75.1229	349	2348	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152215.1	s__Deferrisoma sp013152215	75.1226	93	2348	d__Bacteria;p__Desulfobacterota_C;c__Deferrisomatia;o__Deferrisomatales;f__Deferrisomataceae;g__Deferrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058095.1	s__JABFXX01 sp018058095	75.0745	439	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	99.29	99.24	0.92	0.91	3	-
GCA_001899635.1	s__Labilithrix sp001899635	75.0399	260	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526155.1	s__Deferrisoma camini	75.0387	159	2348	d__Bacteria;p__Desulfobacterota_C;c__Deferrisomatia;o__Deferrisomatales;f__Deferrisomataceae;g__Deferrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	75.037	485	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCF_900104805.1	s__Pseudomonas_K oryzae	74.9887	152	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	74.9845	105	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.9838	488	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218825.1	s__JACRCV01 sp016218825	74.9727	275	2348	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__XYA12-FULL-58-9;g__JACRCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	74.966	211	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344285.1	s__UBA2376 sp002344285	74.9508	415	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997035.1	s__Ralstonia sp007997035	74.9445	66	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	74.941	70	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794545.1	s__JABFXX01 sp016794545	74.929	304	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	74.925	459	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813765.1	s__JABFXX01 sp013813765	74.9195	217	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	74.9054	124	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_000418325.1	s__Sorangium cellulosum_D	74.8787	522	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCF_002950945.1	s__Sorangium cellulosum_E	74.8633	511	2348	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000855665.1	s__Lysobacter sp000855665	74.8499	53	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020205.1	s__Ralstonia pickettii_B	74.8368	60	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	-
GCF_012932665.1	s__Rhizobacter sp012932665	74.8294	229	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397375.1	s__Ralstonia mannitolilytica	74.8125	90	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.68	96.05	0.93	0.87	14	-
GCA_903928345.1	s__CAIYQO01 sp903928345	74.7457	111	2348	d__Bacteria;p__Armatimonadota;c__CAIYQO01;o__CAIYQO01;f__CAIYQO01;g__CAIYQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192835.1	s__PALSA-1004 sp016192835	74.7434	53	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327355.1	s__Pseudomonas_E dryadis	74.7364	95	2348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-29 01:25:16,948] [INFO] GTDB search result was written to GCA_020430745.1_ASM2043074v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:25:16,949] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:25:16,958] [INFO] DFAST_QC result json was written to GCA_020430745.1_ASM2043074v1_genomic.fna/dqc_result.json
[2023-06-29 01:25:16,958] [INFO] DFAST_QC completed!
[2023-06-29 01:25:16,958] [INFO] Total running time: 0h3m46s