[2024-01-24 13:32:42,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference
[2024-01-24 13:32:43,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,779] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c18092-7689-4623-b126-0fbd5317cddc/GCF_007992835.1_ASM799283v1_genomic.fna.gz | prodigal -d GCF_007992835.1_ASM799283v1_genomic.fna/cds.fna -a GCF_007992835.1_ASM799283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:54,083] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:54,083] [INFO] Task started: HMMsearch
[2024-01-24 13:32:54,083] [INFO] Running command: hmmsearch --tblout GCF_007992835.1_ASM799283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/reference_markers.hmm GCF_007992835.1_ASM799283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:54,343] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:54,345] [INFO] Found 6/6 markers.
[2024-01-24 13:32:54,391] [INFO] Query marker FASTA was written to GCF_007992835.1_ASM799283v1_genomic.fna/markers.fasta
[2024-01-24 13:32:54,392] [INFO] Task started: Blastn
[2024-01-24 13:32:54,392] [INFO] Running command: blastn -query GCF_007992835.1_ASM799283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/reference_markers.fasta -out GCF_007992835.1_ASM799283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,665] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,671] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:55,672] [INFO] Target genome list was writen to GCF_007992835.1_ASM799283v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:55,676] [INFO] Task started: fastANI
[2024-01-24 13:32:55,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c18092-7689-4623-b126-0fbd5317cddc/GCF_007992835.1_ASM799283v1_genomic.fna.gz --refList GCF_007992835.1_ASM799283v1_genomic.fna/target_genomes.txt --output GCF_007992835.1_ASM799283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:08,365] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:08,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:08,379] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:08,379] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:08,379] [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
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	87.8797	974	1185	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	87.7759	962	1185	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	85.6017	841	1185	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	84.7229	835	1185	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	84.2816	807	1185	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	83.9985	826	1185	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	81.36	692	1185	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	81.2559	709	1185	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	80.4127	634	1185	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	80.3131	586	1185	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	80.1002	500	1185	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.0379	452	1185	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9943	455	1185	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.9492	428	1185	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.8482	392	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,381] [INFO] DFAST Taxonomy check result was written to GCF_007992835.1_ASM799283v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:08,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:08,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:08,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/checkm_data
[2024-01-24 13:33:08,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:08,423] [INFO] Task started: CheckM
[2024-01-24 13:33:08,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992835.1_ASM799283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992835.1_ASM799283v1_genomic.fna/checkm_input GCF_007992835.1_ASM799283v1_genomic.fna/checkm_result
[2024-01-24 13:34:04,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:04,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:04,254] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:04,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:04,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992835.1_ASM799283v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:04,254] [INFO] Task started: Blastn
[2024-01-24 13:34:04,254] [INFO] Running command: blastn -query GCF_007992835.1_ASM799283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c8ca0cc-667c-4562-916c-aa6fe6a8b2cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992835.1_ASM799283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:06,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:06,185] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:06,186] [INFO] Target genome list was writen to GCF_007992835.1_ASM799283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:06,196] [INFO] Task started: fastANI
[2024-01-24 13:34:06,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c18092-7689-4623-b126-0fbd5317cddc/GCF_007992835.1_ASM799283v1_genomic.fna.gz --refList GCF_007992835.1_ASM799283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992835.1_ASM799283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:15,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:15,011] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:15,011] [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_007992835.1	s__Knoellia locipacati	100.0	1184	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000768675.1	s__Knoellia flava	87.8036	960	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768695.1	s__Knoellia aerolata	85.6149	840	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427985.1	s__Knoellia sp001427985	85.003	836	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768685.1	s__Knoellia subterranea	84.7256	835	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152705.1	s__Knoellia sp000152705	84.5193	952	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	84.2697	808	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768705.1	s__Knoellia sinensis	84.0051	825	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	81.3126	721	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	80.9408	501	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:15,013] [INFO] GTDB search result was written to GCF_007992835.1_ASM799283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:15,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:15,016] [INFO] DFAST_QC result json was written to GCF_007992835.1_ASM799283v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:15,016] [INFO] DFAST_QC completed!
[2024-01-24 13:34:15,017] [INFO] Total running time: 0h1m33s