[2024-01-24 14:22:17,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,265] [INFO] DQC Reference Directory: /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference
[2024-01-24 14:22:18,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,521] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9d2531d-f8d2-4d95-8fdc-2b222594bed2/GCF_014648475.1_ASM1464847v1_genomic.fna.gz | prodigal -d GCF_014648475.1_ASM1464847v1_genomic.fna/cds.fna -a GCF_014648475.1_ASM1464847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:53,210] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:53,211] [INFO] Task started: HMMsearch
[2024-01-24 14:22:53,211] [INFO] Running command: hmmsearch --tblout GCF_014648475.1_ASM1464847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/reference_markers.hmm GCF_014648475.1_ASM1464847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:53,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:53,651] [INFO] Found 6/6 markers.
[2024-01-24 14:22:53,731] [INFO] Query marker FASTA was written to GCF_014648475.1_ASM1464847v1_genomic.fna/markers.fasta
[2024-01-24 14:22:53,731] [INFO] Task started: Blastn
[2024-01-24 14:22:53,731] [INFO] Running command: blastn -query GCF_014648475.1_ASM1464847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/reference_markers.fasta -out GCF_014648475.1_ASM1464847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:55,103] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:55,107] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:55,108] [INFO] Target genome list was writen to GCF_014648475.1_ASM1464847v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:55,116] [INFO] Task started: fastANI
[2024-01-24 14:22:55,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d2531d-f8d2-4d95-8fdc-2b222594bed2/GCF_014648475.1_ASM1464847v1_genomic.fna.gz --refList GCF_014648475.1_ASM1464847v1_genomic.fna/target_genomes.txt --output GCF_014648475.1_ASM1464847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:25,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:25,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:25,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:25,188] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:25,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:25,188] [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 flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	100.0	3155	3160	95	conclusive
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	99.996	3155	3160	95	conclusive
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	93.3949	2469	3160	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	90.8696	2323	3160	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	89.6222	2431	3160	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	89.2381	2155	3160	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	89.1165	2338	3160	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	89.0898	2354	3160	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	87.6371	2167	3160	95	below_threshold
Lentzea fradiae	strain=CGMCC 4.3506	GCA_900100955.1	200378	200378	type	True	86.4813	1937	3160	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.6787	1686	3160	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.9578	844	3160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:25,191] [INFO] DFAST Taxonomy check result was written to GCF_014648475.1_ASM1464847v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:25,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:25,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:25,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/checkm_data
[2024-01-24 14:23:25,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:25,284] [INFO] Task started: CheckM
[2024-01-24 14:23:25,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648475.1_ASM1464847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648475.1_ASM1464847v1_genomic.fna/checkm_input GCF_014648475.1_ASM1464847v1_genomic.fna/checkm_result
[2024-01-24 14:25:41,830] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:41,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:41,861] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:41,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:41,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648475.1_ASM1464847v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:41,862] [INFO] Task started: Blastn
[2024-01-24 14:25:41,863] [INFO] Running command: blastn -query GCF_014648475.1_ASM1464847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89bc06dd-b717-4a4a-b808-a7af79d22d55/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648475.1_ASM1464847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:44,053] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:44,058] [INFO] Selected 12 target genomes.
[2024-01-24 14:25:44,058] [INFO] Target genome list was writen to GCF_014648475.1_ASM1464847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:44,100] [INFO] Task started: fastANI
[2024-01-24 14:25:44,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9d2531d-f8d2-4d95-8fdc-2b222594bed2/GCF_014648475.1_ASM1464847v1_genomic.fna.gz --refList GCF_014648475.1_ASM1464847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648475.1_ASM1464847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:14,618] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:14,634] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:14,635] [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_014648475.1	s__Lentzea flava	100.0	3155	3160	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_016907955.1	s__Lentzea nigeriaca	93.4016	2468	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269295.1	s__Lentzea atacamensis	90.8722	2322	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_003265345.1	s__Lentzea terrae	89.6428	2426	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184385.1	s__Lentzea indica	89.2396	2153	3160	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	89.1063	2385	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	89.0376	2231	3160	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	88.6841	2273	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719115.1	s__Lentzea albidocapillata	87.8537	2077	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.7838	2036	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	87.5198	2122	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100955.1	s__Lentzea fradiae	86.4768	1938	3160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:26:14,637] [INFO] GTDB search result was written to GCF_014648475.1_ASM1464847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:14,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:14,641] [INFO] DFAST_QC result json was written to GCF_014648475.1_ASM1464847v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:14,641] [INFO] DFAST_QC completed!
[2024-01-24 14:26:14,641] [INFO] Total running time: 0h3m57s