[2023-06-19 08:52:46,060] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:52:46,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:52:46,062] [INFO] DQC Reference Directory: /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference
[2023-06-19 08:52:49,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:52:49,864] [INFO] Task started: Prodigal
[2023-06-19 08:52:49,865] [INFO] Running command: gunzip -c /var/lib/cwl/stgd85e4b5e-14bf-4868-bc05-956acc0690ca/GCA_018381075.1_ASM1838107v1_genomic.fna.gz | prodigal -d GCA_018381075.1_ASM1838107v1_genomic.fna/cds.fna -a GCA_018381075.1_ASM1838107v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:52:55,856] [INFO] Task succeeded: Prodigal
[2023-06-19 08:52:55,856] [INFO] Task started: HMMsearch
[2023-06-19 08:52:55,856] [INFO] Running command: hmmsearch --tblout GCA_018381075.1_ASM1838107v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/reference_markers.hmm GCA_018381075.1_ASM1838107v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:52:56,139] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:52:56,141] [INFO] Found 6/6 markers.
[2023-06-19 08:52:56,167] [INFO] Query marker FASTA was written to GCA_018381075.1_ASM1838107v1_genomic.fna/markers.fasta
[2023-06-19 08:52:56,167] [INFO] Task started: Blastn
[2023-06-19 08:52:56,167] [INFO] Running command: blastn -query GCA_018381075.1_ASM1838107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/reference_markers.fasta -out GCA_018381075.1_ASM1838107v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:52:57,024] [INFO] Task succeeded: Blastn
[2023-06-19 08:52:57,028] [INFO] Selected 17 target genomes.
[2023-06-19 08:52:57,029] [INFO] Target genome list was writen to GCA_018381075.1_ASM1838107v1_genomic.fna/target_genomes.txt
[2023-06-19 08:52:57,037] [INFO] Task started: fastANI
[2023-06-19 08:52:57,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgd85e4b5e-14bf-4868-bc05-956acc0690ca/GCA_018381075.1_ASM1838107v1_genomic.fna.gz --refList GCA_018381075.1_ASM1838107v1_genomic.fna/target_genomes.txt --output GCA_018381075.1_ASM1838107v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:53:04,960] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:04,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:53:04,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:53:04,977] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 08:53:04,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:53:04,978] [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 mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	96.5594	677	713	95	conclusive
Rothia aeria	strain=FDAARGOS_1137	GCA_016726365.1	172042	172042	type	True	78.8163	251	713	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	78.65	203	713	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	78.6063	207	713	95	below_threshold
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	78.138	123	713	95	below_threshold
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	78.0343	182	713	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	77.1033	129	713	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	76.9253	102	713	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	76.9237	77	713	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	76.8617	102	713	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	76.5733	67	713	95	below_threshold
Kocuria soli	strain=M5W7-7	GCA_003797835.1	2485125	2485125	type	True	76.5319	90	713	95	below_threshold
Neomicrococcus aestuarii	strain=DSM 105783	GCA_014201135.1	556325	556325	type	True	76.2544	66	713	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	75.9379	55	713	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	75.6581	50	713	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	75.6095	50	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:53:04,980] [INFO] DFAST Taxonomy check result was written to GCA_018381075.1_ASM1838107v1_genomic.fna/tc_result.tsv
[2023-06-19 08:53:04,981] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:53:04,981] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:53:04,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/checkm_data
[2023-06-19 08:53:04,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:53:05,013] [INFO] Task started: CheckM
[2023-06-19 08:53:05,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381075.1_ASM1838107v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381075.1_ASM1838107v1_genomic.fna/checkm_input GCA_018381075.1_ASM1838107v1_genomic.fna/checkm_result
[2023-06-19 08:53:29,257] [INFO] Task succeeded: CheckM
[2023-06-19 08:53:29,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:53:29,289] [INFO] ===== Completeness check finished =====
[2023-06-19 08:53:29,289] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:53:29,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381075.1_ASM1838107v1_genomic.fna/markers.fasta)
[2023-06-19 08:53:29,290] [INFO] Task started: Blastn
[2023-06-19 08:53:29,290] [INFO] Running command: blastn -query GCA_018381075.1_ASM1838107v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga20a436e-890c-4408-b6ea-c70e052004ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381075.1_ASM1838107v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:53:30,625] [INFO] Task succeeded: Blastn
[2023-06-19 08:53:30,635] [INFO] Selected 6 target genomes.
[2023-06-19 08:53:30,635] [INFO] Target genome list was writen to GCA_018381075.1_ASM1838107v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:53:30,640] [INFO] Task started: fastANI
[2023-06-19 08:53:30,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgd85e4b5e-14bf-4868-bc05-956acc0690ca/GCA_018381075.1_ASM1838107v1_genomic.fna.gz --refList GCA_018381075.1_ASM1838107v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381075.1_ASM1838107v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:53:34,243] [INFO] Task succeeded: fastANI
[2023-06-19 08:53:34,256] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:53:34,256] [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_000175615.1	s__Rothia mucilaginosa	96.5594	677	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.99	95.33	0.94	0.89	44	conclusive
GCF_001808955.1	s__Rothia sp001808955	94.8268	661	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCA_015265375.1	s__Rothia sp015265375	94.6165	609	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001548235.1	s__Rothia mucilaginosa_B	94.5184	683	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	-
GCF_001061665.1	s__Rothia mucilaginosa_A	89.0564	624	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_901875305.1	s__Rothia sp902373285	87.9342	600	713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
--------------------------------------------------------------------------------
[2023-06-19 08:53:34,261] [INFO] GTDB search result was written to GCA_018381075.1_ASM1838107v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:53:34,263] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:53:34,269] [INFO] DFAST_QC result json was written to GCA_018381075.1_ASM1838107v1_genomic.fna/dqc_result.json
[2023-06-19 08:53:34,269] [INFO] DFAST_QC completed!
[2023-06-19 08:53:34,269] [INFO] Total running time: 0h0m48s