[2024-01-24 11:27:19,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference
[2024-01-24 11:27:20,350] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,350] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,351] [INFO] Running command: gunzip -c /var/lib/cwl/stge3c70b1a-62c2-479f-8267-d85297efc45d/GCF_003265345.1_ASM326534v1_genomic.fna.gz | prodigal -d GCF_003265345.1_ASM326534v1_genomic.fna/cds.fna -a GCF_003265345.1_ASM326534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:28:03,986] [INFO] Task succeeded: Prodigal
[2024-01-24 11:28:03,987] [INFO] Task started: HMMsearch
[2024-01-24 11:28:03,987] [INFO] Running command: hmmsearch --tblout GCF_003265345.1_ASM326534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/reference_markers.hmm GCF_003265345.1_ASM326534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:28:04,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:28:04,448] [INFO] Found 6/6 markers.
[2024-01-24 11:28:04,535] [INFO] Query marker FASTA was written to GCF_003265345.1_ASM326534v1_genomic.fna/markers.fasta
[2024-01-24 11:28:04,535] [INFO] Task started: Blastn
[2024-01-24 11:28:04,535] [INFO] Running command: blastn -query GCF_003265345.1_ASM326534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/reference_markers.fasta -out GCF_003265345.1_ASM326534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:05,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:05,854] [INFO] Selected 15 target genomes.
[2024-01-24 11:28:05,854] [INFO] Target genome list was writen to GCF_003265345.1_ASM326534v1_genomic.fna/target_genomes.txt
[2024-01-24 11:28:05,866] [INFO] Task started: fastANI
[2024-01-24 11:28:05,866] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c70b1a-62c2-479f-8267-d85297efc45d/GCF_003265345.1_ASM326534v1_genomic.fna.gz --refList GCF_003265345.1_ASM326534v1_genomic.fna/target_genomes.txt --output GCF_003265345.1_ASM326534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:28:43,750] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:43,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:28:43,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:28:43,763] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:28:43,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:28:43,764] [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 terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	100.0	3489	3499	95	conclusive
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	89.636	2437	3499	95	below_threshold
Lentzea flava	strain=JCM 3296	GCA_014648475.1	103732	103732	type	True	89.6146	2416	3499	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	89.5837	2439	3499	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	89.3092	2484	3499	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	89.1494	2546	3499	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	88.7493	2510	3499	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	88.7329	2392	3499	95	below_threshold
Lentzea aerocolonigenes	strain=NBRC 13195	GCA_000974445.1	68170	68170	type	True	88.7274	2524	3499	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.6899	2529	3499	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	87.4966	2222	3499	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	87.4524	2264	3499	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	86.4793	2246	3499	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.5174	1753	3499	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9239	1177	3499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:28:43,766] [INFO] DFAST Taxonomy check result was written to GCF_003265345.1_ASM326534v1_genomic.fna/tc_result.tsv
[2024-01-24 11:28:43,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:28:43,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:28:43,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/checkm_data
[2024-01-24 11:28:43,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:28:43,865] [INFO] Task started: CheckM
[2024-01-24 11:28:43,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003265345.1_ASM326534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003265345.1_ASM326534v1_genomic.fna/checkm_input GCF_003265345.1_ASM326534v1_genomic.fna/checkm_result
[2024-01-24 11:31:35,137] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:35,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:35,164] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:35,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:35,165] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003265345.1_ASM326534v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:35,165] [INFO] Task started: Blastn
[2024-01-24 11:31:35,165] [INFO] Running command: blastn -query GCF_003265345.1_ASM326534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02858268-e80b-4ca1-886d-51820268654d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003265345.1_ASM326534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:37,175] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:37,183] [INFO] Selected 11 target genomes.
[2024-01-24 11:31:37,184] [INFO] Target genome list was writen to GCF_003265345.1_ASM326534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:37,198] [INFO] Task started: fastANI
[2024-01-24 11:31:37,198] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c70b1a-62c2-479f-8267-d85297efc45d/GCF_003265345.1_ASM326534v1_genomic.fna.gz --refList GCF_003265345.1_ASM326534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003265345.1_ASM326534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:06,190] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:06,209] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:06,210] [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_003265345.1	s__Lentzea terrae	100.0	3483	3499	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_003269295.1	s__Lentzea atacamensis	89.6538	2434	3499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_014648475.1	s__Lentzea flava	89.6173	2415	3499	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	89.4801	2319	3499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	89.312	2482	3499	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	89.1425	2547	3499	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	88.7329	2392	3499	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	88.7256	2524	3499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014646255.1	s__Lentzea pudingi	87.5065	2221	3499	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	87.1125	2045	3499	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	86.4775	2247	3499	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 11:32:06,212] [INFO] GTDB search result was written to GCF_003265345.1_ASM326534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:06,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:06,216] [INFO] DFAST_QC result json was written to GCF_003265345.1_ASM326534v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:06,216] [INFO] DFAST_QC completed!
[2024-01-24 11:32:06,216] [INFO] Total running time: 0h4m47s