[2024-01-24 11:12:58,147] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference
[2024-01-24 11:12:59,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,477] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg543ddbb7-2926-4062-b003-4de876ab00da/GCF_002150765.1_ASM215076v1_genomic.fna.gz | prodigal -d GCF_002150765.1_ASM215076v1_genomic.fna/cds.fna -a GCF_002150765.1_ASM215076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:37,309] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:37,310] [INFO] Task started: HMMsearch
[2024-01-24 11:13:37,310] [INFO] Running command: hmmsearch --tblout GCF_002150765.1_ASM215076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/reference_markers.hmm GCF_002150765.1_ASM215076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:37,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:37,775] [INFO] Found 6/6 markers.
[2024-01-24 11:13:37,857] [INFO] Query marker FASTA was written to GCF_002150765.1_ASM215076v1_genomic.fna/markers.fasta
[2024-01-24 11:13:37,857] [INFO] Task started: Blastn
[2024-01-24 11:13:37,857] [INFO] Running command: blastn -query GCF_002150765.1_ASM215076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/reference_markers.fasta -out GCF_002150765.1_ASM215076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:39,156] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:39,160] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:39,161] [INFO] Target genome list was writen to GCF_002150765.1_ASM215076v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:39,171] [INFO] Task started: fastANI
[2024-01-24 11:13:39,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg543ddbb7-2926-4062-b003-4de876ab00da/GCF_002150765.1_ASM215076v1_genomic.fna.gz --refList GCF_002150765.1_ASM215076v1_genomic.fna/target_genomes.txt --output GCF_002150765.1_ASM215076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:24,939] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:24,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:24,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:24,955] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:24,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:24,955] [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 kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	100.0	3266	3275	95	conclusive
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	93.0298	2560	3275	95	below_threshold
Lentzea indica	strain=PSKA42	GCA_012184385.1	2604800	2604800	type	True	89.1984	2148	3275	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	89.1592	2373	3275	95	below_threshold
Lentzea aerocolonigenes	strain=NBRC 13195	GCA_000974445.1	68170	68170	type	True	89.1323	2398	3275	95	below_threshold
Lentzea aerocolonigenes	strain=NRRL B-3298	GCA_000719205.1	68170	68170	type	True	89.1183	2377	3275	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	88.8003	2232	3275	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	88.7583	2264	3275	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	88.7257	2382	3275	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	88.6749	2278	3275	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	88.5368	2243	3275	95	below_threshold
Lentzea albidocapillata	strain=DSM 44073	GCA_900176525.1	40571	40571	type	True	88.4539	2055	3275	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	88.4367	2049	3275	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	88.2071	2159	3275	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	88.1383	2110	3275	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	87.9635	2128	3275	95	below_threshold
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	87.8472	2143	3275	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.4266	1614	3275	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	76.6925	458	3275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:24,958] [INFO] DFAST Taxonomy check result was written to GCF_002150765.1_ASM215076v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:24,959] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:24,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:24,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/checkm_data
[2024-01-24 11:14:24,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:25,055] [INFO] Task started: CheckM
[2024-01-24 11:14:25,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002150765.1_ASM215076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002150765.1_ASM215076v1_genomic.fna/checkm_input GCF_002150765.1_ASM215076v1_genomic.fna/checkm_result
[2024-01-24 11:16:47,719] [INFO] Task succeeded: CheckM
[2024-01-24 11:16:47,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:16:47,745] [INFO] ===== Completeness check finished =====
[2024-01-24 11:16:47,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:16:47,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002150765.1_ASM215076v1_genomic.fna/markers.fasta)
[2024-01-24 11:16:47,746] [INFO] Task started: Blastn
[2024-01-24 11:16:47,747] [INFO] Running command: blastn -query GCF_002150765.1_ASM215076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6571c136-6535-4b40-b2dd-a3bdf3a5691a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002150765.1_ASM215076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:16:49,722] [INFO] Task succeeded: Blastn
[2024-01-24 11:16:49,725] [INFO] Selected 14 target genomes.
[2024-01-24 11:16:49,726] [INFO] Target genome list was writen to GCF_002150765.1_ASM215076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:16:49,736] [INFO] Task started: fastANI
[2024-01-24 11:16:49,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg543ddbb7-2926-4062-b003-4de876ab00da/GCF_002150765.1_ASM215076v1_genomic.fna.gz --refList GCF_002150765.1_ASM215076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002150765.1_ASM215076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:17:24,611] [INFO] Task succeeded: fastANI
[2024-01-24 11:17:24,630] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:17:24,630] [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_002150765.1	s__Lentzea kentuckyensis	100.0	3266	3275	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_011067745.1	s__Lentzea alba	93.041	2558	3275	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	89.1863	2148	3275	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	89.1621	2394	3275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648475.1	s__Lentzea flava	88.7495	2274	3275	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	88.7247	2382	3275	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	88.7006	2194	3275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115955.1	s__Lentzea waywayandensis	88.676	2278	3275	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	88.5203	2245	3275	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	88.4223	2052	3275	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	88.1649	2106	3275	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	87.9857	2124	3275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111005.1	s__Lentzea albida	87.8576	2142	3275	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	86.5801	2055	3275	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 11:17:24,631] [INFO] GTDB search result was written to GCF_002150765.1_ASM215076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:17:24,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:17:24,636] [INFO] DFAST_QC result json was written to GCF_002150765.1_ASM215076v1_genomic.fna/dqc_result.json
[2024-01-24 11:17:24,636] [INFO] DFAST_QC completed!
[2024-01-24 11:17:24,636] [INFO] Total running time: 0h4m26s