[2024-01-25 20:16:20,820] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:20,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:20,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference
[2024-01-25 20:16:22,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:22,061] [INFO] Task started: Prodigal
[2024-01-25 20:16:22,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg29736606-c893-4411-bac2-30cd903f7271/GCF_014646255.1_ASM1464625v1_genomic.fna.gz | prodigal -d GCF_014646255.1_ASM1464625v1_genomic.fna/cds.fna -a GCF_014646255.1_ASM1464625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:48,337] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:48,337] [INFO] Task started: HMMsearch
[2024-01-25 20:16:48,337] [INFO] Running command: hmmsearch --tblout GCF_014646255.1_ASM1464625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/reference_markers.hmm GCF_014646255.1_ASM1464625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:48,724] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:48,724] [INFO] Found 6/6 markers.
[2024-01-25 20:16:48,800] [INFO] Query marker FASTA was written to GCF_014646255.1_ASM1464625v1_genomic.fna/markers.fasta
[2024-01-25 20:16:48,800] [INFO] Task started: Blastn
[2024-01-25 20:16:48,800] [INFO] Running command: blastn -query GCF_014646255.1_ASM1464625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/reference_markers.fasta -out GCF_014646255.1_ASM1464625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:50,061] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:50,066] [INFO] Selected 15 target genomes.
[2024-01-25 20:16:50,066] [INFO] Target genome list was writen to GCF_014646255.1_ASM1464625v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:50,100] [INFO] Task started: fastANI
[2024-01-25 20:16:50,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg29736606-c893-4411-bac2-30cd903f7271/GCF_014646255.1_ASM1464625v1_genomic.fna.gz --refList GCF_014646255.1_ASM1464625v1_genomic.fna/target_genomes.txt --output GCF_014646255.1_ASM1464625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:25,093] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:25,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:25,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:25,104] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:25,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:25,104] [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
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	100.0	3041	3043	95	conclusive
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	91.3911	2345	3043	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	91.3299	2194	3043	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	91.3147	2170	3043	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	91.3049	2364	3043	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	91.2466	2174	3043	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	90.6941	2341	3043	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	90.6728	2312	3043	95	below_threshold
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	90.1437	2290	3043	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	89.0255	2107	3043	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	88.0702	2152	3043	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.0555	2155	3043	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	87.5918	2093	3043	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.2858	1581	3043	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	79.5297	1140	3043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:25,105] [INFO] DFAST Taxonomy check result was written to GCF_014646255.1_ASM1464625v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:25,107] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:25,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:25,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/checkm_data
[2024-01-25 20:17:25,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:25,188] [INFO] Task started: CheckM
[2024-01-25 20:17:25,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646255.1_ASM1464625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646255.1_ASM1464625v1_genomic.fna/checkm_input GCF_014646255.1_ASM1464625v1_genomic.fna/checkm_result
[2024-01-25 20:19:26,361] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:26,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:26,386] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:26,386] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:26,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646255.1_ASM1464625v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:26,387] [INFO] Task started: Blastn
[2024-01-25 20:19:26,387] [INFO] Running command: blastn -query GCF_014646255.1_ASM1464625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42aab46-4fae-44d4-8108-6f5735d6cc5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646255.1_ASM1464625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:28,377] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:28,380] [INFO] Selected 13 target genomes.
[2024-01-25 20:19:28,380] [INFO] Target genome list was writen to GCF_014646255.1_ASM1464625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:28,395] [INFO] Task started: fastANI
[2024-01-25 20:19:28,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg29736606-c893-4411-bac2-30cd903f7271/GCF_014646255.1_ASM1464625v1_genomic.fna.gz --refList GCF_014646255.1_ASM1464625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646255.1_ASM1464625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:00,523] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:00,532] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:00,532] [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_014646255.1	s__Lentzea pudingi	100.0	3041	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000719115.1	s__Lentzea albidocapillata	91.3188	2169	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_003350445.1	s__Lentzea flaviverrucosa	91.2928	2366	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100275.1	s__Lentzea violacea	91.2455	2174	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_900115955.1	s__Lentzea waywayandensis	90.6776	2312	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653695.1	s__Lentzea cavernae	90.6664	2344	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111005.1	s__Lentzea albida	90.0909	2298	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104175.1	s__Lentzea jiangxiensis	89.005	2111	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150765.1	s__Lentzea kentuckyensis	88.1566	2090	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974445.1	s__Lentzea aerocolonigenes	88.0077	2158	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012184385.1	s__Lentzea indica	87.8383	2021	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648475.1	s__Lentzea flava	87.5864	2099	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	87.527	2012	3043	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:00,534] [INFO] GTDB search result was written to GCF_014646255.1_ASM1464625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:00,534] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:00,538] [INFO] DFAST_QC result json was written to GCF_014646255.1_ASM1464625v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:00,538] [INFO] DFAST_QC completed!
[2024-01-25 20:20:00,538] [INFO] Total running time: 0h3m40s