[2024-01-24 12:36:20,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:20,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:20,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference
[2024-01-24 12:36:22,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:22,206] [INFO] Task started: Prodigal
[2024-01-24 12:36:22,207] [INFO] Running command: gunzip -c /var/lib/cwl/stge8fbc53a-a9fc-4482-9d65-7f543dd8034a/GCF_018332695.1_ASM1833269v1_genomic.fna.gz | prodigal -d GCF_018332695.1_ASM1833269v1_genomic.fna/cds.fna -a GCF_018332695.1_ASM1833269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:51,680] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:51,680] [INFO] Task started: HMMsearch
[2024-01-24 12:36:51,680] [INFO] Running command: hmmsearch --tblout GCF_018332695.1_ASM1833269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/reference_markers.hmm GCF_018332695.1_ASM1833269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:52,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:52,107] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge8fbc53a-a9fc-4482-9d65-7f543dd8034a/GCF_018332695.1_ASM1833269v1_genomic.fna.gz]
[2024-01-24 12:36:52,190] [INFO] Query marker FASTA was written to GCF_018332695.1_ASM1833269v1_genomic.fna/markers.fasta
[2024-01-24 12:36:52,190] [INFO] Task started: Blastn
[2024-01-24 12:36:52,190] [INFO] Running command: blastn -query GCF_018332695.1_ASM1833269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/reference_markers.fasta -out GCF_018332695.1_ASM1833269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:53,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:53,495] [INFO] Selected 19 target genomes.
[2024-01-24 12:36:53,495] [INFO] Target genome list was writen to GCF_018332695.1_ASM1833269v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:53,506] [INFO] Task started: fastANI
[2024-01-24 12:36:53,507] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fbc53a-a9fc-4482-9d65-7f543dd8034a/GCF_018332695.1_ASM1833269v1_genomic.fna.gz --refList GCF_018332695.1_ASM1833269v1_genomic.fna/target_genomes.txt --output GCF_018332695.1_ASM1833269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:38,688] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:38,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:38,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:38,715] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:38,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:38,715] [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 toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	100.0	3513	3529	95	conclusive
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	90.9843	2711	3529	95	below_threshold
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	87.6036	2452	3529	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	85.2858	2144	3529	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	84.0162	2188	3529	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	83.5423	2082	3529	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	82.1102	1984	3529	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	81.9614	1965	3529	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	81.8652	1777	3529	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	81.0528	1488	3529	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	80.9459	1549	3529	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	80.8928	1562	3529	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.6387	1664	3529	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8869	855	3529	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.7254	1029	3529	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.4441	1321	3529	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.3873	1462	3529	95	below_threshold
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	76.854	889	3529	95	below_threshold
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	76.7653	904	3529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:38,717] [INFO] DFAST Taxonomy check result was written to GCF_018332695.1_ASM1833269v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:38,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:38,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:38,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/checkm_data
[2024-01-24 12:37:38,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:38,820] [INFO] Task started: CheckM
[2024-01-24 12:37:38,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018332695.1_ASM1833269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018332695.1_ASM1833269v1_genomic.fna/checkm_input GCF_018332695.1_ASM1833269v1_genomic.fna/checkm_result
[2024-01-24 12:39:06,819] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:06,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:06,845] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:06,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:06,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018332695.1_ASM1833269v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:06,846] [INFO] Task started: Blastn
[2024-01-24 12:39:06,846] [INFO] Running command: blastn -query GCF_018332695.1_ASM1833269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d700da-8b78-4788-98bd-84d6f622e8bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_018332695.1_ASM1833269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:08,904] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:08,909] [INFO] Selected 10 target genomes.
[2024-01-24 12:39:08,910] [INFO] Target genome list was writen to GCF_018332695.1_ASM1833269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:08,918] [INFO] Task started: fastANI
[2024-01-24 12:39:08,918] [INFO] Running command: fastANI --query /var/lib/cwl/stge8fbc53a-a9fc-4482-9d65-7f543dd8034a/GCF_018332695.1_ASM1833269v1_genomic.fna.gz --refList GCF_018332695.1_ASM1833269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018332695.1_ASM1833269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:39,603] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:39,615] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:39,616] [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_018332695.1	s__Actinoplanes toevensis	100.0	3513	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862435.1	s__Actinoplanes tereljensis	91.008	2707	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862175.1	s__Actinoplanes durhamensis	87.6337	2446	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862195.1	s__Actinoplanes ferrugineus	85.2627	2149	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379645.1	s__Actinoplanes globisporus	83.9894	2195	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	83.5285	2087	3529	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	82.9807	1931	3529	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	82.0723	1996	3529	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	81.9857	1959	3529	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	81.9012	1797	3529	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:39,618] [INFO] GTDB search result was written to GCF_018332695.1_ASM1833269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:39,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:39,628] [INFO] DFAST_QC result json was written to GCF_018332695.1_ASM1833269v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:39,628] [INFO] DFAST_QC completed!
[2024-01-24 12:39:39,628] [INFO] Total running time: 0h3m19s