[2024-01-24 10:47:10,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference
[2024-01-24 10:47:12,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,099] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg44b4290e-fd65-45de-8b39-e4aa79263567/GCF_016907955.1_ASM1690795v1_genomic.fna.gz | prodigal -d GCF_016907955.1_ASM1690795v1_genomic.fna/cds.fna -a GCF_016907955.1_ASM1690795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:41,299] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:41,299] [INFO] Task started: HMMsearch
[2024-01-24 10:47:41,299] [INFO] Running command: hmmsearch --tblout GCF_016907955.1_ASM1690795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/reference_markers.hmm GCF_016907955.1_ASM1690795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:41,739] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:41,740] [INFO] Found 6/6 markers.
[2024-01-24 10:47:41,817] [INFO] Query marker FASTA was written to GCF_016907955.1_ASM1690795v1_genomic.fna/markers.fasta
[2024-01-24 10:47:41,817] [INFO] Task started: Blastn
[2024-01-24 10:47:41,817] [INFO] Running command: blastn -query GCF_016907955.1_ASM1690795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/reference_markers.fasta -out GCF_016907955.1_ASM1690795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:43,160] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:43,164] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:43,164] [INFO] Target genome list was writen to GCF_016907955.1_ASM1690795v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:43,303] [INFO] Task started: fastANI
[2024-01-24 10:47:43,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg44b4290e-fd65-45de-8b39-e4aa79263567/GCF_016907955.1_ASM1690795v1_genomic.fna.gz --refList GCF_016907955.1_ASM1690795v1_genomic.fna/target_genomes.txt --output GCF_016907955.1_ASM1690795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:16,586] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:16,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:16,602] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:16,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:16,603] [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 nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	100.0	3091	3093	95	conclusive
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	93.3597	2458	3093	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	93.3546	2458	3093	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	90.3635	2227	3093	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	89.4706	2449	3093	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.9973	2388	3093	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	88.9639	2140	3093	95	below_threshold
Lentzea xinjiangensis	strain=CGMCC 4.3525	GCA_900110955.1	402600	402600	type	True	87.5971	1955	3093	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	87.3769	2117	3093	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	87.1716	2075	3093	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	86.3566	2081	3093	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.5716	1661	3093	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.2003	839	3093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,604] [INFO] DFAST Taxonomy check result was written to GCF_016907955.1_ASM1690795v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:16,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:16,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:16,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/checkm_data
[2024-01-24 10:48:16,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:16,693] [INFO] Task started: CheckM
[2024-01-24 10:48:16,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907955.1_ASM1690795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907955.1_ASM1690795v1_genomic.fna/checkm_input GCF_016907955.1_ASM1690795v1_genomic.fna/checkm_result
[2024-01-24 10:50:15,818] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:15,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:15,845] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:15,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:15,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907955.1_ASM1690795v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:15,846] [INFO] Task started: Blastn
[2024-01-24 10:50:15,846] [INFO] Running command: blastn -query GCF_016907955.1_ASM1690795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e225d61-73db-40a2-952c-210934e4edfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907955.1_ASM1690795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:17,904] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:17,915] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:17,915] [INFO] Target genome list was writen to GCF_016907955.1_ASM1690795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:17,924] [INFO] Task started: fastANI
[2024-01-24 10:50:17,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg44b4290e-fd65-45de-8b39-e4aa79263567/GCF_016907955.1_ASM1690795v1_genomic.fna.gz --refList GCF_016907955.1_ASM1690795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907955.1_ASM1690795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:46,850] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:46,868] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:46,869] [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_016907955.1	s__Lentzea nigeriaca	100.0	3091	3093	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_014648475.1	s__Lentzea flava	93.3838	2454	3093	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	90.3611	2228	3093	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	89.4652	2450	3093	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	88.9952	2410	3093	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	88.9749	2139	3093	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	88.8288	2137	3093	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	87.5851	1957	3093	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	87.1996	2070	3093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	86.4425	2032	3093	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	86.3686	2078	3093	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 10:50:46,873] [INFO] GTDB search result was written to GCF_016907955.1_ASM1690795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:46,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:46,877] [INFO] DFAST_QC result json was written to GCF_016907955.1_ASM1690795v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:46,877] [INFO] DFAST_QC completed!
[2024-01-24 10:50:46,877] [INFO] Total running time: 0h3m37s