[2024-01-25 19:48:05,499] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference
[2024-01-25 19:48:06,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,648] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d42912a-0290-435c-9d7b-043544963181/GCF_016127495.1_ASM1612749v1_genomic.fna.gz | prodigal -d GCF_016127495.1_ASM1612749v1_genomic.fna/cds.fna -a GCF_016127495.1_ASM1612749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:14,619] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:14,619] [INFO] Task started: HMMsearch
[2024-01-25 19:48:14,619] [INFO] Running command: hmmsearch --tblout GCF_016127495.1_ASM1612749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/reference_markers.hmm GCF_016127495.1_ASM1612749v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:14,802] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:14,803] [INFO] Found 6/6 markers.
[2024-01-25 19:48:14,826] [INFO] Query marker FASTA was written to GCF_016127495.1_ASM1612749v1_genomic.fna/markers.fasta
[2024-01-25 19:48:14,827] [INFO] Task started: Blastn
[2024-01-25 19:48:14,827] [INFO] Running command: blastn -query GCF_016127495.1_ASM1612749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/reference_markers.fasta -out GCF_016127495.1_ASM1612749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:15,906] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:15,909] [INFO] Selected 15 target genomes.
[2024-01-25 19:48:15,909] [INFO] Target genome list was writen to GCF_016127495.1_ASM1612749v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:15,914] [INFO] Task started: fastANI
[2024-01-25 19:48:15,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d42912a-0290-435c-9d7b-043544963181/GCF_016127495.1_ASM1612749v1_genomic.fna.gz --refList GCF_016127495.1_ASM1612749v1_genomic.fna/target_genomes.txt --output GCF_016127495.1_ASM1612749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:25,843] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:25,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:25,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:25,854] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:48:25,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:25,854] [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
Kytococcus sedentarius	strain=FDAARGOS_1061	GCA_016127495.1	1276	1276	type	True	100.0	927	927	95	conclusive
Kytococcus sedentarius	strain=NCTC11040	GCA_900452405.1	1276	1276	type	True	99.9986	926	927	95	conclusive
Kytococcus sedentarius	strain=DSM 20547	GCA_000023925.1	1276	1276	type	True	99.9947	924	927	95	conclusive
Kytococcus aerolatus	strain=DSM 22179	GCA_900187395.1	592308	592308	type	True	84.068	612	927	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	78.6111	333	927	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	78.2701	295	927	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	78.1383	294	927	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	78.1292	291	927	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.0725	293	927	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	78.03	291	927	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.9113	269	927	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	77.8676	279	927	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.8464	184	927	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	77.8276	297	927	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	77.6807	247	927	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:25,856] [INFO] DFAST Taxonomy check result was written to GCF_016127495.1_ASM1612749v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:25,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:25,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:25,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/checkm_data
[2024-01-25 19:48:25,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:25,888] [INFO] Task started: CheckM
[2024-01-25 19:48:25,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127495.1_ASM1612749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127495.1_ASM1612749v1_genomic.fna/checkm_input GCF_016127495.1_ASM1612749v1_genomic.fna/checkm_result
[2024-01-25 19:49:42,173] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:42,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:42,192] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:42,192] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:42,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127495.1_ASM1612749v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:42,194] [INFO] Task started: Blastn
[2024-01-25 19:49:42,194] [INFO] Running command: blastn -query GCF_016127495.1_ASM1612749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg832db2ad-4f32-463f-83c6-0cebab0cad9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127495.1_ASM1612749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:44,073] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:44,076] [INFO] Selected 15 target genomes.
[2024-01-25 19:49:44,076] [INFO] Target genome list was writen to GCF_016127495.1_ASM1612749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:44,103] [INFO] Task started: fastANI
[2024-01-25 19:49:44,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d42912a-0290-435c-9d7b-043544963181/GCF_016127495.1_ASM1612749v1_genomic.fna.gz --refList GCF_016127495.1_ASM1612749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127495.1_ASM1612749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:53,458] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:53,470] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:53,470] [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_000023925.1	s__Kytococcus sedentarius	99.9947	924	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	98.33	96.37	0.94	0.84	5	conclusive
GCF_002847825.1	s__Kytococcus schroeteri	84.5015	600	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	99.14	99.06	0.95	0.94	3	-
GCF_900187395.1	s__Kytococcus aerolatus	84.0402	614	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	78.5975	331	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.5857	292	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	78.4446	304	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003721155.3	s__Marihabitans melonis	78.1787	267	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_006337125.1	s__Serinicoccus chungangensis	78.095	296	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	77.9423	252	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	77.8574	311	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153545.1	s__Serinicoccus sediminis	77.8269	297	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	77.7883	242	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326735.1	s__Phycicoccus endophyticus	77.7076	246	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCA_014763705.1	s__Phycicoccus sp014763705	77.4381	198	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	77.429	300	927	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:53,478] [INFO] GTDB search result was written to GCF_016127495.1_ASM1612749v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:53,482] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:53,486] [INFO] DFAST_QC result json was written to GCF_016127495.1_ASM1612749v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:53,486] [INFO] DFAST_QC completed!
[2024-01-25 19:49:53,486] [INFO] Total running time: 0h1m48s