[2024-01-24 13:32:41,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference
[2024-01-24 13:32:42,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,388] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cf11560-e530-4372-8caa-2f7d10a081ab/GCF_023717965.1_ASM2371796v1_genomic.fna.gz | prodigal -d GCF_023717965.1_ASM2371796v1_genomic.fna/cds.fna -a GCF_023717965.1_ASM2371796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:13,800] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:13,801] [INFO] Task started: HMMsearch
[2024-01-24 13:33:13,801] [INFO] Running command: hmmsearch --tblout GCF_023717965.1_ASM2371796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/reference_markers.hmm GCF_023717965.1_ASM2371796v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:14,207] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:14,208] [INFO] Found 6/6 markers.
[2024-01-24 13:33:14,282] [INFO] Query marker FASTA was written to GCF_023717965.1_ASM2371796v1_genomic.fna/markers.fasta
[2024-01-24 13:33:14,283] [INFO] Task started: Blastn
[2024-01-24 13:33:14,283] [INFO] Running command: blastn -query GCF_023717965.1_ASM2371796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/reference_markers.fasta -out GCF_023717965.1_ASM2371796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:15,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:15,470] [INFO] Selected 12 target genomes.
[2024-01-24 13:33:15,471] [INFO] Target genome list was writen to GCF_023717965.1_ASM2371796v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:15,475] [INFO] Task started: fastANI
[2024-01-24 13:33:15,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf11560-e530-4372-8caa-2f7d10a081ab/GCF_023717965.1_ASM2371796v1_genomic.fna.gz --refList GCF_023717965.1_ASM2371796v1_genomic.fna/target_genomes.txt --output GCF_023717965.1_ASM2371796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:43,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:43,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:43,360] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:43,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:43,360] [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
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	85.3785	2216	3404	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	85.2386	2230	3404	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	85.1792	2141	3404	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	85.0719	2126	3404	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	85.0221	2157	3404	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	84.8865	2209	3404	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.2523	1956	3404	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.5739	1520	3404	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8564	807	3404	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6185	1066	3404	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	78.5325	975	3404	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.458	1232	3404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,362] [INFO] DFAST Taxonomy check result was written to GCF_023717965.1_ASM2371796v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:43,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:43,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:43,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/checkm_data
[2024-01-24 13:33:43,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:43,454] [INFO] Task started: CheckM
[2024-01-24 13:33:43,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023717965.1_ASM2371796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023717965.1_ASM2371796v1_genomic.fna/checkm_input GCF_023717965.1_ASM2371796v1_genomic.fna/checkm_result
[2024-01-24 13:35:33,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:33,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:33,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:33,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:33,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023717965.1_ASM2371796v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:33,350] [INFO] Task started: Blastn
[2024-01-24 13:35:33,350] [INFO] Running command: blastn -query GCF_023717965.1_ASM2371796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13578e4d-0d3f-40ec-bf38-7e9dcf859ce0/dqc_reference/reference_markers_gtdb.fasta -out GCF_023717965.1_ASM2371796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:35,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:35,146] [INFO] Selected 8 target genomes.
[2024-01-24 13:35:35,146] [INFO] Target genome list was writen to GCF_023717965.1_ASM2371796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:35,150] [INFO] Task started: fastANI
[2024-01-24 13:35:35,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cf11560-e530-4372-8caa-2f7d10a081ab/GCF_023717965.1_ASM2371796v1_genomic.fna.gz --refList GCF_023717965.1_ASM2371796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023717965.1_ASM2371796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:56,631] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:56,637] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:35:56,637] [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_016785085.1	s__Actinoplanes sp016785085	85.3936	2213	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016834655.1	s__Actinoplanes sp016834655	85.238	2230	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	85.1979	2136	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018829635.1	s__Actinoplanes bogorensis	85.0401	2132	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.9469	2154	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362215.1	s__Actinoplanes brasiliensis	84.8592	2218	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862115.1	s__Actinoplanes deccanensis	83.2273	1963	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	81.8336	1733	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:56,638] [INFO] GTDB search result was written to GCF_023717965.1_ASM2371796v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:56,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:56,641] [INFO] DFAST_QC result json was written to GCF_023717965.1_ASM2371796v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:56,641] [INFO] DFAST_QC completed!
[2024-01-24 13:35:56,641] [INFO] Total running time: 0h3m15s