[2023-06-18 20:11:05,120] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:11:05,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:11:05,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference
[2023-06-18 20:11:07,470] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:11:07,471] [INFO] Task started: Prodigal
[2023-06-18 20:11:07,471] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd36c207-da18-442e-9272-a4855767bcc9/GCA_014846925.1_ASM1484692v1_genomic.fna.gz | prodigal -d GCA_014846925.1_ASM1484692v1_genomic.fna/cds.fna -a GCA_014846925.1_ASM1484692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:11:11,838] [INFO] Task succeeded: Prodigal
[2023-06-18 20:11:11,839] [INFO] Task started: HMMsearch
[2023-06-18 20:11:11,839] [INFO] Running command: hmmsearch --tblout GCA_014846925.1_ASM1484692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/reference_markers.hmm GCA_014846925.1_ASM1484692v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:11:12,065] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:11:12,067] [INFO] Found 6/6 markers.
[2023-06-18 20:11:12,106] [INFO] Query marker FASTA was written to GCA_014846925.1_ASM1484692v1_genomic.fna/markers.fasta
[2023-06-18 20:11:12,106] [INFO] Task started: Blastn
[2023-06-18 20:11:12,107] [INFO] Running command: blastn -query GCA_014846925.1_ASM1484692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/reference_markers.fasta -out GCA_014846925.1_ASM1484692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:11:13,044] [INFO] Task succeeded: Blastn
[2023-06-18 20:11:13,048] [INFO] Selected 22 target genomes.
[2023-06-18 20:11:13,048] [INFO] Target genome list was writen to GCA_014846925.1_ASM1484692v1_genomic.fna/target_genomes.txt
[2023-06-18 20:11:13,056] [INFO] Task started: fastANI
[2023-06-18 20:11:13,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd36c207-da18-442e-9272-a4855767bcc9/GCA_014846925.1_ASM1484692v1_genomic.fna.gz --refList GCA_014846925.1_ASM1484692v1_genomic.fna/target_genomes.txt --output GCA_014846925.1_ASM1484692v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:11:23,479] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:23,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:11:23,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:11:23,502] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:11:23,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:11:23,503] [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	87.7968	430	497	95	below_threshold
Rothia aeria	strain=FDAARGOS_1137	GCA_016726365.1	172042	172042	type	True	78.6866	172	497	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	78.5973	134	497	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	78.5967	134	497	95	below_threshold
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	78.0941	130	497	95	below_threshold
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	77.9117	86	497	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.1698	95	497	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	77.1578	95	497	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	77.1439	95	497	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	76.9708	62	497	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	76.7295	70	497	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	76.6695	56	497	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	76.6689	74	497	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	76.6473	53	497	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	76.6432	74	497	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	76.2559	59	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:11:23,505] [INFO] DFAST Taxonomy check result was written to GCA_014846925.1_ASM1484692v1_genomic.fna/tc_result.tsv
[2023-06-18 20:11:23,506] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:11:23,506] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:11:23,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/checkm_data
[2023-06-18 20:11:23,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:11:23,531] [INFO] Task started: CheckM
[2023-06-18 20:11:23,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014846925.1_ASM1484692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014846925.1_ASM1484692v1_genomic.fna/checkm_input GCA_014846925.1_ASM1484692v1_genomic.fna/checkm_result
[2023-06-18 20:11:43,327] [INFO] Task succeeded: CheckM
[2023-06-18 20:11:43,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:11:43,349] [INFO] ===== Completeness check finished =====
[2023-06-18 20:11:43,350] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:11:43,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014846925.1_ASM1484692v1_genomic.fna/markers.fasta)
[2023-06-18 20:11:43,350] [INFO] Task started: Blastn
[2023-06-18 20:11:43,351] [INFO] Running command: blastn -query GCA_014846925.1_ASM1484692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87458c2b-2ca6-4f97-a102-d31175fbe774/dqc_reference/reference_markers_gtdb.fasta -out GCA_014846925.1_ASM1484692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:11:44,708] [INFO] Task succeeded: Blastn
[2023-06-18 20:11:44,716] [INFO] Selected 6 target genomes.
[2023-06-18 20:11:44,716] [INFO] Target genome list was writen to GCA_014846925.1_ASM1484692v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:11:44,720] [INFO] Task started: fastANI
[2023-06-18 20:11:44,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd36c207-da18-442e-9272-a4855767bcc9/GCA_014846925.1_ASM1484692v1_genomic.fna.gz --refList GCA_014846925.1_ASM1484692v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014846925.1_ASM1484692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:11:47,847] [INFO] Task succeeded: fastANI
[2023-06-18 20:11:47,859] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:11:47,859] [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_901875305.1	s__Rothia sp902373285	97.9377	482	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	conclusive
GCF_001061665.1	s__Rothia mucilaginosa_A	91.1357	453	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_001808955.1	s__Rothia sp001808955	87.9588	438	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCF_001548235.1	s__Rothia mucilaginosa_B	87.8986	439	497	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	87.7968	430	497	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	87.7823	433	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-18 20:11:47,861] [INFO] GTDB search result was written to GCA_014846925.1_ASM1484692v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:11:47,862] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:11:47,865] [INFO] DFAST_QC result json was written to GCA_014846925.1_ASM1484692v1_genomic.fna/dqc_result.json
[2023-06-18 20:11:47,865] [INFO] DFAST_QC completed!
[2023-06-18 20:11:47,866] [INFO] Total running time: 0h0m43s