[2024-01-24 11:34:41,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference
[2024-01-24 11:34:42,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,851] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,851] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe8a35ed-2ca7-446d-9dc0-89948b06c320/GCF_024137025.1_ASM2413702v1_genomic.fna.gz | prodigal -d GCF_024137025.1_ASM2413702v1_genomic.fna/cds.fna -a GCF_024137025.1_ASM2413702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:12,362] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:12,362] [INFO] Task started: HMMsearch
[2024-01-24 11:35:12,362] [INFO] Running command: hmmsearch --tblout GCF_024137025.1_ASM2413702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/reference_markers.hmm GCF_024137025.1_ASM2413702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:12,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:12,889] [INFO] Found 6/6 markers.
[2024-01-24 11:35:12,995] [INFO] Query marker FASTA was written to GCF_024137025.1_ASM2413702v1_genomic.fna/markers.fasta
[2024-01-24 11:35:12,998] [INFO] Task started: Blastn
[2024-01-24 11:35:12,998] [INFO] Running command: blastn -query GCF_024137025.1_ASM2413702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/reference_markers.fasta -out GCF_024137025.1_ASM2413702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:14,325] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:14,328] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:14,329] [INFO] Target genome list was writen to GCF_024137025.1_ASM2413702v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:14,335] [INFO] Task started: fastANI
[2024-01-24 11:35:14,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe8a35ed-2ca7-446d-9dc0-89948b06c320/GCF_024137025.1_ASM2413702v1_genomic.fna.gz --refList GCF_024137025.1_ASM2413702v1_genomic.fna/target_genomes.txt --output GCF_024137025.1_ASM2413702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,757] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,769] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:46,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:46,770] [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	85.5352	2360	3290	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	85.4008	2342	3290	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	85.3352	2246	3290	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	85.1333	2243	3290	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	85.044	2121	3290	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	85.0159	2131	3290	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	83.2447	2054	3290	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.0143	1989	3290	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	81.7709	1861	3290	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.3077	1500	3290	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.6147	968	3290	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.374	1105	3290	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	76.1315	673	3290	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	75.988	706	3290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,771] [INFO] DFAST Taxonomy check result was written to GCF_024137025.1_ASM2413702v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,772] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/checkm_data
[2024-01-24 11:35:46,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,860] [INFO] Task started: CheckM
[2024-01-24 11:35:46,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024137025.1_ASM2413702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024137025.1_ASM2413702v1_genomic.fna/checkm_input GCF_024137025.1_ASM2413702v1_genomic.fna/checkm_result
[2024-01-24 11:37:11,554] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:11,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:11,576] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:11,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:11,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024137025.1_ASM2413702v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:11,577] [INFO] Task started: Blastn
[2024-01-24 11:37:11,577] [INFO] Running command: blastn -query GCF_024137025.1_ASM2413702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fd16ca2-6d56-4403-a1bd-15332e514197/dqc_reference/reference_markers_gtdb.fasta -out GCF_024137025.1_ASM2413702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:13,409] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:13,413] [INFO] Selected 8 target genomes.
[2024-01-24 11:37:13,413] [INFO] Target genome list was writen to GCF_024137025.1_ASM2413702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:13,426] [INFO] Task started: fastANI
[2024-01-24 11:37:13,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe8a35ed-2ca7-446d-9dc0-89948b06c320/GCF_024137025.1_ASM2413702v1_genomic.fna.gz --refList GCF_024137025.1_ASM2413702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024137025.1_ASM2413702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:35,473] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:35,481] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:37:35,482] [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	85.5466	2357	3290	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	85.4384	2333	3290	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	85.3565	2244	3290	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	85.1585	2237	3290	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	85.0119	2132	3290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.8079	2120	3290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	83.2286	2058	3290	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	82.963	2001	3290	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 11:37:35,483] [INFO] GTDB search result was written to GCF_024137025.1_ASM2413702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:35,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:35,487] [INFO] DFAST_QC result json was written to GCF_024137025.1_ASM2413702v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:35,487] [INFO] DFAST_QC completed!
[2024-01-24 11:37:35,487] [INFO] Total running time: 0h2m54s