[2023-06-28 14:40:26,221] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:40:26,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:40:26,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference
[2023-06-28 14:40:27,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:40:27,335] [INFO] Task started: Prodigal
[2023-06-28 14:40:27,335] [INFO] Running command: gunzip -c /var/lib/cwl/stgd959651c-0549-4a21-8272-22bd03e74909/GCA_020850435.1_ASM2085043v1_genomic.fna.gz | prodigal -d GCA_020850435.1_ASM2085043v1_genomic.fna/cds.fna -a GCA_020850435.1_ASM2085043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:40:48,916] [INFO] Task succeeded: Prodigal
[2023-06-28 14:40:48,916] [INFO] Task started: HMMsearch
[2023-06-28 14:40:48,916] [INFO] Running command: hmmsearch --tblout GCA_020850435.1_ASM2085043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/reference_markers.hmm GCA_020850435.1_ASM2085043v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:40:49,275] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:40:49,277] [INFO] Found 6/6 markers.
[2023-06-28 14:40:49,338] [INFO] Query marker FASTA was written to GCA_020850435.1_ASM2085043v1_genomic.fna/markers.fasta
[2023-06-28 14:40:49,338] [INFO] Task started: Blastn
[2023-06-28 14:40:49,338] [INFO] Running command: blastn -query GCA_020850435.1_ASM2085043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/reference_markers.fasta -out GCA_020850435.1_ASM2085043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:40:50,024] [INFO] Task succeeded: Blastn
[2023-06-28 14:40:50,028] [INFO] Selected 34 target genomes.
[2023-06-28 14:40:50,029] [INFO] Target genome list was writen to GCA_020850435.1_ASM2085043v1_genomic.fna/target_genomes.txt
[2023-06-28 14:40:50,037] [INFO] Task started: fastANI
[2023-06-28 14:40:50,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgd959651c-0549-4a21-8272-22bd03e74909/GCA_020850435.1_ASM2085043v1_genomic.fna.gz --refList GCA_020850435.1_ASM2085043v1_genomic.fna/target_genomes.txt --output GCA_020850435.1_ASM2085043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:41:20,007] [INFO] Task succeeded: fastANI
[2023-06-28 14:41:20,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:41:20,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:41:20,026] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:41:20,026] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:41:20,027] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.3628	402	2870	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.2586	262	2870	95	below_threshold
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	75.243	52	2870	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.2208	238	2870	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	75.2063	98	2870	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1687	255	2870	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	75.1431	124	2870	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.0618	101	2870	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	75.0363	166	2870	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.0264	239	2870	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.0229	123	2870	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	74.9855	146	2870	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	74.9797	155	2870	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.978	269	2870	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9751	239	2870	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	74.9723	145	2870	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9429	299	2870	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9325	243	2870	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.9275	474	2870	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	74.8917	73	2870	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	74.8883	230	2870	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	74.8867	165	2870	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	74.8439	150	2870	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	74.8422	174	2870	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	74.8419	145	2870	95	below_threshold
Terrimesophilobacter mesophilus	strain=DSM 19267	GCA_014200375.1	433647	433647	type	True	74.8348	69	2870	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	74.825	89	2870	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	74.7986	116	2870	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	74.7638	140	2870	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	74.7209	213	2870	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	74.7164	233	2870	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	74.7134	176	2870	95	below_threshold
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	74.5636	77	2870	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:41:20,029] [INFO] DFAST Taxonomy check result was written to GCA_020850435.1_ASM2085043v1_genomic.fna/tc_result.tsv
[2023-06-28 14:41:20,029] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:41:20,029] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:41:20,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/checkm_data
[2023-06-28 14:41:20,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:41:20,115] [INFO] Task started: CheckM
[2023-06-28 14:41:20,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020850435.1_ASM2085043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020850435.1_ASM2085043v1_genomic.fna/checkm_input GCA_020850435.1_ASM2085043v1_genomic.fna/checkm_result
[2023-06-28 14:43:02,262] [INFO] Task succeeded: CheckM
[2023-06-28 14:43:02,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:43:02,286] [INFO] ===== Completeness check finished =====
[2023-06-28 14:43:02,286] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:43:02,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020850435.1_ASM2085043v1_genomic.fna/markers.fasta)
[2023-06-28 14:43:02,287] [INFO] Task started: Blastn
[2023-06-28 14:43:02,287] [INFO] Running command: blastn -query GCA_020850435.1_ASM2085043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd2a8881-ce96-4b82-8bff-c64129b729d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_020850435.1_ASM2085043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:43:03,347] [INFO] Task succeeded: Blastn
[2023-06-28 14:43:03,349] [INFO] Selected 33 target genomes.
[2023-06-28 14:43:03,350] [INFO] Target genome list was writen to GCA_020850435.1_ASM2085043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:43:03,391] [INFO] Task started: fastANI
[2023-06-28 14:43:03,391] [INFO] Running command: fastANI --query /var/lib/cwl/stgd959651c-0549-4a21-8272-22bd03e74909/GCA_020850435.1_ASM2085043v1_genomic.fna.gz --refList GCA_020850435.1_ASM2085043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020850435.1_ASM2085043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:43:36,728] [INFO] Task succeeded: fastANI
[2023-06-28 14:43:36,746] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:43:36,746] [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_011526105.1	s__WYAZ01 sp011526105	76.5067	352	2870	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__WYAZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703535.1	s__JADJBV01 sp016703535	76.4173	435	2870	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__JADJBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003490025.1	s__Geomonas sp003490025	75.4391	67	2870	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904005.1	s__CAIOAK01 sp903904005	75.431	199	2870	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.78	99.64	0.94	0.92	4	-
GCA_003242475.1	s__ZC4RG40 sp003242475	75.3072	144	2870	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__ZC4RG40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	75.2925	301	2870	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCA_016218825.1	s__JACRCV01 sp016218825	75.2822	327	2870	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_000017505.1	s__Anaeromyxobacter sp000017505	75.2591	406	2870	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018986935.1	s__Geomonas sp018986935	75.2387	97	2870	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	99.24	99.10	0.94	0.94	3	-
GCF_016458235.1	s__Geomonas propionica	75.1894	97	2870	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279285.1	s__RBG-13-68-16 sp002279285	75.182	113	2870	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	98.89	98.89	0.79	0.79	2	-
GCA_016717005.1	s__UBA2376 sp016717005	75.173	667	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	75.154	771	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.1484	596	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCF_001482195.1	s__Luteimonas abyssi	75.1391	124	2870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003555285.1	s__Thioalkalivibrio_B sp003555285	75.1333	66	2870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	75.1249	725	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_003170275.1	s__PALSA-1104 sp003170275	75.1188	455	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__PALSA-1104	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	75.0652	101	2870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	75.051	167	2870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_001931535.1	s__Minicystis rosea	75.0051	640	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050235.1	s__UTPRO1 sp002050235	74.979	221	2870	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__UTPRO1	95.0	99.98	99.98	0.96	0.96	2	-
GCF_900104805.1	s__Pseudomonas_K oryzae	74.9776	156	2870	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_902826555.1	s__Hyphomicrobium sp902826555	74.9701	100	2870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298115.1	s__RBG-13-68-16 sp004298115	74.9263	175	2870	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	74.9212	710	2870	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133645.1	s__RBG-13-68-16 sp003133645	74.8333	139	2870	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826755.1	s__JABFSM01 sp902826755	74.8275	93	2870	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JABFSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	74.7618	192	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	74.7065	233	2870	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:43:36,747] [INFO] GTDB search result was written to GCA_020850435.1_ASM2085043v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:43:36,748] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:43:36,753] [INFO] DFAST_QC result json was written to GCA_020850435.1_ASM2085043v1_genomic.fna/dqc_result.json
[2023-06-28 14:43:36,753] [INFO] DFAST_QC completed!
[2023-06-28 14:43:36,753] [INFO] Total running time: 0h3m11s