[2024-01-25 17:52:36,240] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference
[2024-01-25 17:52:37,473] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:37,474] [INFO] Task started: Prodigal
[2024-01-25 17:52:37,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0e03d2-87b1-4f48-8f64-5326816d7317/GCF_016726365.1_ASM1672636v1_genomic.fna.gz | prodigal -d GCF_016726365.1_ASM1672636v1_genomic.fna/cds.fna -a GCF_016726365.1_ASM1672636v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:44,099] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:44,100] [INFO] Task started: HMMsearch
[2024-01-25 17:52:44,100] [INFO] Running command: hmmsearch --tblout GCF_016726365.1_ASM1672636v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/reference_markers.hmm GCF_016726365.1_ASM1672636v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:44,292] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:44,294] [INFO] Found 6/6 markers.
[2024-01-25 17:52:44,316] [INFO] Query marker FASTA was written to GCF_016726365.1_ASM1672636v1_genomic.fna/markers.fasta
[2024-01-25 17:52:44,316] [INFO] Task started: Blastn
[2024-01-25 17:52:44,316] [INFO] Running command: blastn -query GCF_016726365.1_ASM1672636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/reference_markers.fasta -out GCF_016726365.1_ASM1672636v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:45,048] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:45,052] [INFO] Selected 18 target genomes.
[2024-01-25 17:52:45,053] [INFO] Target genome list was writen to GCF_016726365.1_ASM1672636v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:45,064] [INFO] Task started: fastANI
[2024-01-25 17:52:45,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0e03d2-87b1-4f48-8f64-5326816d7317/GCF_016726365.1_ASM1672636v1_genomic.fna.gz --refList GCF_016726365.1_ASM1672636v1_genomic.fna/target_genomes.txt --output GCF_016726365.1_ASM1672636v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:54,411] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:54,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:54,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:54,419] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:54,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:54,419] [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 aeria	strain=FDAARGOS_1137	GCA_016726365.1	172042	172042	type	True	100.0	860	861	95	conclusive
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	85.81	412	861	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	85.7968	418	861	95	below_threshold
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	78.977	266	861	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	77.778	75	861	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	77.556	70	861	95	below_threshold
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	77.4596	116	861	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.2986	74	861	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	76.6864	71	861	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	76.6221	57	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:54,420] [INFO] DFAST Taxonomy check result was written to GCF_016726365.1_ASM1672636v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:54,421] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:54,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:54,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/checkm_data
[2024-01-25 17:52:54,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:54,450] [INFO] Task started: CheckM
[2024-01-25 17:52:54,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016726365.1_ASM1672636v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016726365.1_ASM1672636v1_genomic.fna/checkm_input GCF_016726365.1_ASM1672636v1_genomic.fna/checkm_result
[2024-01-25 17:53:17,387] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:17,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:17,406] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:17,406] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:17,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016726365.1_ASM1672636v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:17,407] [INFO] Task started: Blastn
[2024-01-25 17:53:17,407] [INFO] Running command: blastn -query GCF_016726365.1_ASM1672636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddd50ca4-1a83-4c7d-ae21-a8621fc72245/dqc_reference/reference_markers_gtdb.fasta -out GCF_016726365.1_ASM1672636v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:18,500] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:18,503] [INFO] Selected 15 target genomes.
[2024-01-25 17:53:18,503] [INFO] Target genome list was writen to GCF_016726365.1_ASM1672636v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:18,516] [INFO] Task started: fastANI
[2024-01-25 17:53:18,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0e03d2-87b1-4f48-8f64-5326816d7317/GCF_016726365.1_ASM1672636v1_genomic.fna.gz --refList GCF_016726365.1_ASM1672636v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016726365.1_ASM1672636v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:26,642] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:26,649] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:26,650] [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_002355935.1	s__Rothia aeria	99.9372	860	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.65	97.24	0.95	0.93	14	conclusive
GCF_000164695.2	s__Rothia dentocariosa	85.7795	419	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.76	96.24	0.94	0.87	27	-
GCF_001061665.1	s__Rothia mucilaginosa_A	79.1218	263	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_001548235.1	s__Rothia mucilaginosa_B	79.0869	275	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	-
GCF_000175615.1	s__Rothia mucilaginosa	78.9838	266	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.99	95.33	0.94	0.89	44	-
GCA_015265375.1	s__Rothia sp015265375	78.9803	260	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001808955.1	s__Rothia sp001808955	78.9695	265	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCF_901875305.1	s__Rothia sp902373285	78.8386	257	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
GCF_001570865.1	s__Rothia kristinae	77.2986	74	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCF_004136635.1	s__Rothia halotolerans	77.2475	82	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831305.1	s__Kocuria coralli	76.6445	58	861	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:26,651] [INFO] GTDB search result was written to GCF_016726365.1_ASM1672636v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:26,651] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:26,655] [INFO] DFAST_QC result json was written to GCF_016726365.1_ASM1672636v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:26,655] [INFO] DFAST_QC completed!
[2024-01-25 17:53:26,655] [INFO] Total running time: 0h0m50s