[2024-01-24 14:03:08,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference
[2024-01-24 14:03:09,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,880] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a5648de-043d-4269-8245-d9ba49c2519d/GCF_014635585.1_ASM1463558v1_genomic.fna.gz | prodigal -d GCF_014635585.1_ASM1463558v1_genomic.fna/cds.fna -a GCF_014635585.1_ASM1463558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:16,562] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:16,563] [INFO] Task started: HMMsearch
[2024-01-24 14:03:16,563] [INFO] Running command: hmmsearch --tblout GCF_014635585.1_ASM1463558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/reference_markers.hmm GCF_014635585.1_ASM1463558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:16,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:16,852] [INFO] Found 6/6 markers.
[2024-01-24 14:03:16,895] [INFO] Query marker FASTA was written to GCF_014635585.1_ASM1463558v1_genomic.fna/markers.fasta
[2024-01-24 14:03:16,896] [INFO] Task started: Blastn
[2024-01-24 14:03:16,896] [INFO] Running command: blastn -query GCF_014635585.1_ASM1463558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/reference_markers.fasta -out GCF_014635585.1_ASM1463558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:17,803] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:17,806] [INFO] Selected 27 target genomes.
[2024-01-24 14:03:17,807] [INFO] Target genome list was writen to GCF_014635585.1_ASM1463558v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:17,839] [INFO] Task started: fastANI
[2024-01-24 14:03:17,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5648de-043d-4269-8245-d9ba49c2519d/GCF_014635585.1_ASM1463558v1_genomic.fna.gz --refList GCF_014635585.1_ASM1463558v1_genomic.fna/target_genomes.txt --output GCF_014635585.1_ASM1463558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:35,432] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:35,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:35,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:35,450] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:35,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:35,451] [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
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	100.0	816	817	95	conclusive
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	78.9185	198	817	95	below_threshold
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	78.4328	181	817	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	77.6893	131	817	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	77.6619	128	817	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.6574	128	817	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.2541	90	817	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.2507	89	817	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	77.1542	90	817	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	77.1542	90	817	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	77.047	130	817	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	77.0403	62	817	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	77.0285	90	817	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	76.9374	101	817	95	below_threshold
Paenarthrobacter histidinolovorans	strain=JCM 2520	GCA_014647595.1	43664	43664	type	True	76.9105	70	817	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	76.8505	96	817	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	76.8467	115	817	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	76.808	126	817	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	76.8012	129	817	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	76.779	131	817	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	76.7279	61	817	95	below_threshold
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	76.5952	55	817	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	76.5925	88	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:35,453] [INFO] DFAST Taxonomy check result was written to GCF_014635585.1_ASM1463558v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:35,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:35,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:35,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/checkm_data
[2024-01-24 14:03:35,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:35,487] [INFO] Task started: CheckM
[2024-01-24 14:03:35,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635585.1_ASM1463558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635585.1_ASM1463558v1_genomic.fna/checkm_input GCF_014635585.1_ASM1463558v1_genomic.fna/checkm_result
[2024-01-24 14:04:01,364] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:01,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:01,384] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:01,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:01,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635585.1_ASM1463558v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:01,386] [INFO] Task started: Blastn
[2024-01-24 14:04:01,386] [INFO] Running command: blastn -query GCF_014635585.1_ASM1463558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a67aa85-51d7-40bf-adb0-2b92e332fb3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635585.1_ASM1463558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:02,578] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:02,582] [INFO] Selected 20 target genomes.
[2024-01-24 14:04:02,582] [INFO] Target genome list was writen to GCF_014635585.1_ASM1463558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:02,639] [INFO] Task started: fastANI
[2024-01-24 14:04:02,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5648de-043d-4269-8245-d9ba49c2519d/GCF_014635585.1_ASM1463558v1_genomic.fna.gz --refList GCF_014635585.1_ASM1463558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635585.1_ASM1463558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:12,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:12,783] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:12,783] [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_014635585.1	s__Rothia aerolata	100.0	816	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019115985.1	s__Rothia avicola	79.2788	292	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004569295.1	s__Rothia nasimurium_B	79.1397	307	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014217215.1	s__Rothia nasimurium_C	79.0775	314	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.36	98.36	0.95	0.95	2	-
GCF_012396615.1	s__Rothia terrae	78.9098	199	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.55	98.48	0.95	0.93	4	-
GCF_014705945.2	s__Rothia amarae	78.8829	190	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.68	98.63	0.96	0.95	3	-
GCF_002087015.1	s__Rothia nasimurium_A	78.8642	272	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418375.1	s__Rothia sp002418375	78.6445	201	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.17	96.17	0.93	0.93	2	-
GCF_001548235.1	s__Rothia mucilaginosa_B	78.2675	187	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	-
GCF_016924835.1	s__Rothia sp016924835	78.2395	188	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.38	99.38	0.96	0.96	2	-
GCF_001808955.1	s__Rothia sp001808955	78.1845	185	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCA_002492045.1	s__Rothia sp002492045	77.9197	165	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012163155.1	s__Kocuria subflava	77.0489	96	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.27	98.56	0.95	0.91	3	-
GCF_004217565.1	s__Zhihengliuella halotolerans	77.0403	62	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_001046895.1	s__Pseudarthrobacter siccitolerans	77.0285	90	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907795.1	s__Kocuria palustris	76.8467	115	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.24	97.70	0.90	0.87	15	-
GCF_001863355.1	s__Paeniglutamicibacter sp001863355	76.8114	90	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028095.1	s__Paenarthrobacter ureafaciens	76.8078	72	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.49	97.15	0.88	0.82	19	-
GCF_014636775.1	s__Kocuria dechangensis	76.7617	132	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003575975.1	s__Galactobacter valiniphilus	76.5925	88	817	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:12,785] [INFO] GTDB search result was written to GCF_014635585.1_ASM1463558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:12,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:12,790] [INFO] DFAST_QC result json was written to GCF_014635585.1_ASM1463558v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:12,791] [INFO] DFAST_QC completed!
[2024-01-24 14:04:12,791] [INFO] Total running time: 0h1m5s