[2024-01-24 14:46:35,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference
[2024-01-24 14:46:36,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,643] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg05eaa704-8409-46e2-b9de-188da8ff4d13/GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/cds.fna -a GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:15,999] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:15,999] [INFO] Task started: HMMsearch
[2024-01-24 14:47:15,999] [INFO] Running command: hmmsearch --tblout GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/reference_markers.hmm GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:16,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:16,470] [INFO] Found 6/6 markers.
[2024-01-24 14:47:16,553] [INFO] Query marker FASTA was written to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:16,554] [INFO] Task started: Blastn
[2024-01-24 14:47:16,554] [INFO] Running command: blastn -query GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/reference_markers.fasta -out GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:17,924] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:17,928] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:17,928] [INFO] Target genome list was writen to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:17,935] [INFO] Task started: fastANI
[2024-01-24 14:47:17,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg05eaa704-8409-46e2-b9de-188da8ff4d13/GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna.gz --refList GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:02,194] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:02,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:02,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:02,220] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:02,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:02,221] [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 albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	100.0	3123	3128	95	conclusive
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	91.4718	2530	3128	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	90.1657	2283	3128	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	90.0233	2358	3128	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	89.9787	2321	3128	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	89.9236	2136	3128	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	89.9063	2168	3128	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	89.8703	2149	3128	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	89.4368	2170	3128	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	88.0547	2175	3128	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	87.9465	2114	3128	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	87.9327	2224	3128	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	87.7895	2138	3128	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	87.3947	2146	3128	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	87.1964	2211	3128	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	86.6867	2213	3128	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.3967	1643	3128	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	77.7574	900	3128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:02,224] [INFO] DFAST Taxonomy check result was written to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:48:02,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:02,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:02,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/checkm_data
[2024-01-24 14:48:02,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:02,331] [INFO] Task started: CheckM
[2024-01-24 14:48:02,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/checkm_input GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:50:32,311] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:32,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:32,336] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:32,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:32,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:50:32,337] [INFO] Task started: Blastn
[2024-01-24 14:50:32,338] [INFO] Running command: blastn -query GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg02af9a59-0ed6-451d-aaa4-6f6c186894bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:34,491] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:34,495] [INFO] Selected 14 target genomes.
[2024-01-24 14:50:34,496] [INFO] Target genome list was writen to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:34,507] [INFO] Task started: fastANI
[2024-01-24 14:50:34,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg05eaa704-8409-46e2-b9de-188da8ff4d13/GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna.gz --refList GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:09,782] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:09,796] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:09,796] [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_900111005.1	s__Lentzea albida	100.0	3123	3128	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_014653695.1	s__Lentzea cavernae	91.4536	2533	3128	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	90.1954	2278	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350445.1	s__Lentzea flaviverrucosa	90.0325	2356	3128	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	89.9053	2139	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_000719115.1	s__Lentzea albidocapillata	89.8729	2149	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900104175.1	s__Lentzea jiangxiensis	89.4295	2171	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	88.0684	2173	3128	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	87.9143	2120	3128	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	87.7893	2136	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265345.1	s__Lentzea terrae	87.1968	2212	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001701025.1	s__Lentzea guizhouensis	86.6856	2213	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007845675.1	s__Lentzea sp007845675	82.3916	1645	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	79.8674	1263	3128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:09,798] [INFO] GTDB search result was written to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:09,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:09,802] [INFO] DFAST_QC result json was written to GCF_900111005.1_IMG-taxon_2619619034_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:51:09,802] [INFO] DFAST_QC completed!
[2024-01-24 14:51:09,802] [INFO] Total running time: 0h4m34s