[2024-01-24 12:47:49,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:49,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:49,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference
[2024-01-24 12:47:50,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,903] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b56c1ed-155e-433a-ad14-37b882535762/GCF_024171845.1_ASM2417184v1_genomic.fna.gz | prodigal -d GCF_024171845.1_ASM2417184v1_genomic.fna/cds.fna -a GCF_024171845.1_ASM2417184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:25,163] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:25,163] [INFO] Task started: HMMsearch
[2024-01-24 12:48:25,163] [INFO] Running command: hmmsearch --tblout GCF_024171845.1_ASM2417184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/reference_markers.hmm GCF_024171845.1_ASM2417184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:25,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:25,600] [INFO] Found 6/6 markers.
[2024-01-24 12:48:25,685] [INFO] Query marker FASTA was written to GCF_024171845.1_ASM2417184v1_genomic.fna/markers.fasta
[2024-01-24 12:48:25,686] [INFO] Task started: Blastn
[2024-01-24 12:48:25,686] [INFO] Running command: blastn -query GCF_024171845.1_ASM2417184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/reference_markers.fasta -out GCF_024171845.1_ASM2417184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:27,012] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:27,016] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:27,016] [INFO] Target genome list was writen to GCF_024171845.1_ASM2417184v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:27,022] [INFO] Task started: fastANI
[2024-01-24 12:48:27,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b56c1ed-155e-433a-ad14-37b882535762/GCF_024171845.1_ASM2417184v1_genomic.fna.gz --refList GCF_024171845.1_ASM2417184v1_genomic.fna/target_genomes.txt --output GCF_024171845.1_ASM2417184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:58,093] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:58,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:58,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:58,104] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:48:58,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:58,104] [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 flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	100.0	3175	3185	95	conclusive
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	99.9833	3115	3185	95	conclusive
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	93.4132	2476	3185	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	90.802	2350	3185	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	89.5886	2431	3185	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	89.254	2144	3185	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	89.1397	2335	3185	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	89.0861	2361	3185	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	87.5966	2170	3185	95	below_threshold
Lentzea fradiae	strain=CGMCC 4.3506	GCA_900100955.1	200378	200378	type	True	86.4397	1962	3185	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.6136	1715	3185	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	77.8863	854	3185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:58,106] [INFO] DFAST Taxonomy check result was written to GCF_024171845.1_ASM2417184v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:58,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:58,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:58,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/checkm_data
[2024-01-24 12:48:58,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:58,196] [INFO] Task started: CheckM
[2024-01-24 12:48:58,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171845.1_ASM2417184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171845.1_ASM2417184v1_genomic.fna/checkm_input GCF_024171845.1_ASM2417184v1_genomic.fna/checkm_result
[2024-01-24 12:51:15,281] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:15,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:15,309] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:15,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:15,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171845.1_ASM2417184v1_genomic.fna/markers.fasta)
[2024-01-24 12:51:15,311] [INFO] Task started: Blastn
[2024-01-24 12:51:15,311] [INFO] Running command: blastn -query GCF_024171845.1_ASM2417184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d0c347b-d3a0-4567-a611-9254507c4838/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171845.1_ASM2417184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:17,348] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:17,352] [INFO] Selected 12 target genomes.
[2024-01-24 12:51:17,353] [INFO] Target genome list was writen to GCF_024171845.1_ASM2417184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:51:17,380] [INFO] Task started: fastANI
[2024-01-24 12:51:17,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b56c1ed-155e-433a-ad14-37b882535762/GCF_024171845.1_ASM2417184v1_genomic.fna.gz --refList GCF_024171845.1_ASM2417184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171845.1_ASM2417184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:47,416] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:47,431] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:47,431] [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	99.9833	3115	3185	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	93.3959	2478	3185	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	90.8053	2349	3185	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	89.5966	2430	3185	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	89.2392	2146	3185	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	89.1382	2369	3185	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	89.0343	2255	3185	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	88.7889	2271	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	87.8188	2038	3185	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	87.7355	2098	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_014646255.1	s__Lentzea pudingi	87.5856	2108	3185	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	86.4642	1959	3185	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 12:51:47,433] [INFO] GTDB search result was written to GCF_024171845.1_ASM2417184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:47,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:47,438] [INFO] DFAST_QC result json was written to GCF_024171845.1_ASM2417184v1_genomic.fna/dqc_result.json
[2024-01-24 12:51:47,439] [INFO] DFAST_QC completed!
[2024-01-24 12:51:47,439] [INFO] Total running time: 0h3m58s