[2024-01-25 20:19:20,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference
[2024-01-25 20:19:21,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,837] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c4225c8-f33a-4675-97bf-641b39af8271/GCF_016862435.1_ASM1686243v1_genomic.fna.gz | prodigal -d GCF_016862435.1_ASM1686243v1_genomic.fna/cds.fna -a GCF_016862435.1_ASM1686243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:54,568] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:54,569] [INFO] Task started: HMMsearch
[2024-01-25 20:19:54,569] [INFO] Running command: hmmsearch --tblout GCF_016862435.1_ASM1686243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/reference_markers.hmm GCF_016862435.1_ASM1686243v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:54,928] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:54,929] [INFO] Found 6/6 markers.
[2024-01-25 20:19:55,006] [INFO] Query marker FASTA was written to GCF_016862435.1_ASM1686243v1_genomic.fna/markers.fasta
[2024-01-25 20:19:55,006] [INFO] Task started: Blastn
[2024-01-25 20:19:55,007] [INFO] Running command: blastn -query GCF_016862435.1_ASM1686243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/reference_markers.fasta -out GCF_016862435.1_ASM1686243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:56,251] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:56,254] [INFO] Selected 22 target genomes.
[2024-01-25 20:19:56,254] [INFO] Target genome list was writen to GCF_016862435.1_ASM1686243v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:56,264] [INFO] Task started: fastANI
[2024-01-25 20:19:56,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c4225c8-f33a-4675-97bf-641b39af8271/GCF_016862435.1_ASM1686243v1_genomic.fna.gz --refList GCF_016862435.1_ASM1686243v1_genomic.fna/target_genomes.txt --output GCF_016862435.1_ASM1686243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:47,770] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:47,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:47,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:47,785] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:47,785] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:47,785] [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 tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	100.0	3552	3556	95	conclusive
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	90.965	2717	3556	95	below_threshold
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	87.6185	2585	3556	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	85.324	2091	3556	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	83.8213	2168	3556	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	83.4678	2102	3556	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	82.9443	1995	3556	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	82.1547	1950	3556	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	82.041	1998	3556	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	81.9496	1928	3556	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	81.8631	1995	3556	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	81.7402	1752	3556	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.7385	1630	3556	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8385	847	3556	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	78.8053	1113	3556	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8052	1018	3556	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	78.6303	1190	3556	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	78.4748	953	3556	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	78.4648	959	3556	95	below_threshold
Micromonospora globbae	strain=WPS1-2	GCA_003610785.1	1894969	1894969	type	True	78.2324	1085	3556	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.5852	1421	3556	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.4735	1298	3556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:47,787] [INFO] DFAST Taxonomy check result was written to GCF_016862435.1_ASM1686243v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:47,788] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:47,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:47,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/checkm_data
[2024-01-25 20:20:47,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:47,891] [INFO] Task started: CheckM
[2024-01-25 20:20:47,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862435.1_ASM1686243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862435.1_ASM1686243v1_genomic.fna/checkm_input GCF_016862435.1_ASM1686243v1_genomic.fna/checkm_result
[2024-01-25 20:22:25,064] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:25,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:25,094] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:25,094] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:25,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862435.1_ASM1686243v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:25,096] [INFO] Task started: Blastn
[2024-01-25 20:22:25,096] [INFO] Running command: blastn -query GCF_016862435.1_ASM1686243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccc9873-4b42-46f3-a0f7-d9607c3c30f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862435.1_ASM1686243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:27,093] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:27,096] [INFO] Selected 13 target genomes.
[2024-01-25 20:22:27,096] [INFO] Target genome list was writen to GCF_016862435.1_ASM1686243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:27,106] [INFO] Task started: fastANI
[2024-01-25 20:22:27,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c4225c8-f33a-4675-97bf-641b39af8271/GCF_016862435.1_ASM1686243v1_genomic.fna.gz --refList GCF_016862435.1_ASM1686243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862435.1_ASM1686243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:03,645] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:03,656] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:03,656] [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_016862435.1	s__Actinoplanes tereljensis	100.0	3552	3556	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_018332695.1	s__Actinoplanes toevensis	90.9711	2716	3556	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	87.6358	2580	3556	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	85.3292	2091	3556	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	83.8453	2161	3556	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	83.4546	2106	3556	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	82.9577	1990	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785085.1	s__Actinoplanes sp016785085	82.1687	1946	3556	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	82.0489	1996	3556	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	81.9352	1932	3556	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	81.8397	2001	3556	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	81.6662	1786	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018397995.1	s__NBRC-107566 sp018397995	78.1395	1006	3556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:03,658] [INFO] GTDB search result was written to GCF_016862435.1_ASM1686243v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:03,659] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:03,662] [INFO] DFAST_QC result json was written to GCF_016862435.1_ASM1686243v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:03,663] [INFO] DFAST_QC completed!
[2024-01-25 20:23:03,663] [INFO] Total running time: 0h3m43s