[2023-06-30 14:11:23,282] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:11:23,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:11:23,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference
[2023-06-30 14:11:24,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:11:24,479] [INFO] Task started: Prodigal
[2023-06-30 14:11:24,479] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8c59c36-c1e1-43ae-bf34-30e8b0032865/GCA_016708135.1_ASM1670813v1_genomic.fna.gz | prodigal -d GCA_016708135.1_ASM1670813v1_genomic.fna/cds.fna -a GCA_016708135.1_ASM1670813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:11:51,137] [INFO] Task succeeded: Prodigal
[2023-06-30 14:11:51,138] [INFO] Task started: HMMsearch
[2023-06-30 14:11:51,138] [INFO] Running command: hmmsearch --tblout GCA_016708135.1_ASM1670813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/reference_markers.hmm GCA_016708135.1_ASM1670813v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:11:51,511] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:11:51,512] [INFO] Found 6/6 markers.
[2023-06-30 14:11:51,577] [INFO] Query marker FASTA was written to GCA_016708135.1_ASM1670813v1_genomic.fna/markers.fasta
[2023-06-30 14:11:51,577] [INFO] Task started: Blastn
[2023-06-30 14:11:51,578] [INFO] Running command: blastn -query GCA_016708135.1_ASM1670813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/reference_markers.fasta -out GCA_016708135.1_ASM1670813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:52,364] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:52,369] [INFO] Selected 34 target genomes.
[2023-06-30 14:11:52,369] [INFO] Target genome list was writen to GCA_016708135.1_ASM1670813v1_genomic.fna/target_genomes.txt
[2023-06-30 14:11:52,374] [INFO] Task started: fastANI
[2023-06-30 14:11:52,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c59c36-c1e1-43ae-bf34-30e8b0032865/GCA_016708135.1_ASM1670813v1_genomic.fna.gz --refList GCA_016708135.1_ASM1670813v1_genomic.fna/target_genomes.txt --output GCA_016708135.1_ASM1670813v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:12:21,349] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:21,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:12:21,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:12:21,377] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:12:21,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:12:21,378] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.6705	642	2638	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.6592	254	2638	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.4863	108	2638	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.383	451	2638	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.3761	172	2638	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.3568	96	2638	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.3108	369	2638	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	75.2981	145	2638	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.2419	251	2638	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.2223	405	2638	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2069	361	2638	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.1885	180	2638	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.1792	262	2638	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.1714	194	2638	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	75.1621	94	2638	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.1497	190	2638	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.1025	175	2638	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	75.1012	126	2638	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	75.0571	115	2638	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.036	194	2638	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	74.9913	246	2638	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	74.9872	102	2638	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	74.9714	96	2638	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	74.9627	99	2638	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.9605	95	2638	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	74.9545	96	2638	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	74.9519	301	2638	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	74.9405	273	2638	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	74.9196	333	2638	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	74.9162	280	2638	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.9111	356	2638	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	74.8578	113	2638	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	74.8342	322	2638	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	74.8226	165	2638	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:12:21,380] [INFO] DFAST Taxonomy check result was written to GCA_016708135.1_ASM1670813v1_genomic.fna/tc_result.tsv
[2023-06-30 14:12:21,380] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:12:21,380] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:12:21,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/checkm_data
[2023-06-30 14:12:21,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:12:21,457] [INFO] Task started: CheckM
[2023-06-30 14:12:21,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708135.1_ASM1670813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708135.1_ASM1670813v1_genomic.fna/checkm_input GCA_016708135.1_ASM1670813v1_genomic.fna/checkm_result
[2023-06-30 14:14:15,945] [INFO] Task succeeded: CheckM
[2023-06-30 14:14:15,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:14:15,970] [INFO] ===== Completeness check finished =====
[2023-06-30 14:14:15,970] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:14:15,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708135.1_ASM1670813v1_genomic.fna/markers.fasta)
[2023-06-30 14:14:15,971] [INFO] Task started: Blastn
[2023-06-30 14:14:15,971] [INFO] Running command: blastn -query GCA_016708135.1_ASM1670813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cadf05c-91d7-4338-bab9-a1af941a658c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708135.1_ASM1670813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:14:17,280] [INFO] Task succeeded: Blastn
[2023-06-30 14:14:17,285] [INFO] Selected 24 target genomes.
[2023-06-30 14:14:17,286] [INFO] Target genome list was writen to GCA_016708135.1_ASM1670813v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:14:17,296] [INFO] Task started: fastANI
[2023-06-30 14:14:17,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c59c36-c1e1-43ae-bf34-30e8b0032865/GCA_016708135.1_ASM1670813v1_genomic.fna.gz --refList GCA_016708135.1_ASM1670813v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708135.1_ASM1670813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:14:42,325] [INFO] Task succeeded: fastANI
[2023-06-30 14:14:42,347] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:14:42,347] [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_016706685.1	s__JADJJE01 sp016706685	99.2128	2392	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	conclusive
GCA_012744445.1	s__JAAYBZ01 sp012744445	76.9831	409	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009992505.1	s__JAADHO01 sp009992505	76.8584	268	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	76.5101	507	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.5096	656	2638	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	-
GCA_013151775.1	s__JAADHO01 sp013151775	76.4623	367	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644045.1	s__UBA1660 sp017644045	76.4416	527	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647035.1	s__SG8-38 sp003647035	75.9613	102	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	-
GCA_004283055.1	s__SG8-38 sp004283055	75.9194	131	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	-
GCA_017881185.1	s__JADGRF01 sp017881185	75.836	269	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881055.1	s__JADGRF01 sp017881055	75.815	243	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002645.1	s__SG8-38 sp013002645	75.7794	92	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214955.1	s__JACRMN01 sp016214955	75.4693	302	2638	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	75.4116	335	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904885.1	s__Melittangium primigenium	75.3993	386	2638	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	75.2173	467	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	75.2095	571	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_001899635.1	s__Labilithrix sp001899635	75.1699	334	2638	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	75.1433	164	2638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_017308985.1	s__Lysobacter sp017308985	75.055	163	2638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003387805.1	s__ZC3RG10 sp003387805	74.9517	63	2638	d__Bacteria;p__Firmicutes_G;c__Limnochordia;o__Limnochordales_A;f__ZCTH02-B6;g__ZC3RG10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331415.1	s__DSRV01 sp011331415	74.85	239	2638	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__DSRV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:14:42,350] [INFO] GTDB search result was written to GCA_016708135.1_ASM1670813v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:14:42,350] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:14:42,357] [INFO] DFAST_QC result json was written to GCA_016708135.1_ASM1670813v1_genomic.fna/dqc_result.json
[2023-06-30 14:14:42,357] [INFO] DFAST_QC completed!
[2023-06-30 14:14:42,357] [INFO] Total running time: 0h3m19s