[2024-01-25 20:27:20,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference
[2024-01-25 20:27:21,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,741] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg5af02191-78f1-4b6d-8f0c-02c4aaeaf857/GCF_016862115.1_ASM1686211v1_genomic.fna.gz | prodigal -d GCF_016862115.1_ASM1686211v1_genomic.fna/cds.fna -a GCF_016862115.1_ASM1686211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:50,813] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:50,813] [INFO] Task started: HMMsearch
[2024-01-25 20:27:50,814] [INFO] Running command: hmmsearch --tblout GCF_016862115.1_ASM1686211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/reference_markers.hmm GCF_016862115.1_ASM1686211v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:51,229] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:51,232] [INFO] Found 6/6 markers.
[2024-01-25 20:27:51,321] [INFO] Query marker FASTA was written to GCF_016862115.1_ASM1686211v1_genomic.fna/markers.fasta
[2024-01-25 20:27:51,321] [INFO] Task started: Blastn
[2024-01-25 20:27:51,321] [INFO] Running command: blastn -query GCF_016862115.1_ASM1686211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/reference_markers.fasta -out GCF_016862115.1_ASM1686211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:52,517] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:52,520] [INFO] Selected 19 target genomes.
[2024-01-25 20:27:52,520] [INFO] Target genome list was writen to GCF_016862115.1_ASM1686211v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:52,532] [INFO] Task started: fastANI
[2024-01-25 20:27:52,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af02191-78f1-4b6d-8f0c-02c4aaeaf857/GCF_016862115.1_ASM1686211v1_genomic.fna.gz --refList GCF_016862115.1_ASM1686211v1_genomic.fna/target_genomes.txt --output GCF_016862115.1_ASM1686211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:36,748] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:36,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:36,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:36,760] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:36,761] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:36,761] [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 deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	100.0	3414	3430	95	conclusive
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	87.1078	2590	3430	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	83.2803	2019	3430	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	83.1282	1895	3430	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	83.0719	1929	3430	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	83.0242	1971	3430	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	82.901	2089	3430	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	82.6435	1975	3430	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	81.9613	1941	3430	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	80.9239	1757	3430	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	80.8354	1822	3430	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.7448	1634	3430	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.895	1060	3430	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6367	1056	3430	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.5169	1292	3430	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.2117	800	3430	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	76.0755	758	3430	95	below_threshold
Kytococcus aerolatus	strain=DSM 22179	GCA_900187395.1	592308	592308	type	True	76.0497	282	3430	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	75.7666	1025	3430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:36,762] [INFO] DFAST Taxonomy check result was written to GCF_016862115.1_ASM1686211v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:36,763] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:36,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:36,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/checkm_data
[2024-01-25 20:28:36,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:36,861] [INFO] Task started: CheckM
[2024-01-25 20:28:36,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862115.1_ASM1686211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862115.1_ASM1686211v1_genomic.fna/checkm_input GCF_016862115.1_ASM1686211v1_genomic.fna/checkm_result
[2024-01-25 20:30:41,188] [INFO] Task succeeded: CheckM
[2024-01-25 20:30:41,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:30:41,213] [INFO] ===== Completeness check finished =====
[2024-01-25 20:30:41,213] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:30:41,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862115.1_ASM1686211v1_genomic.fna/markers.fasta)
[2024-01-25 20:30:41,214] [INFO] Task started: Blastn
[2024-01-25 20:30:41,214] [INFO] Running command: blastn -query GCF_016862115.1_ASM1686211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20993c3b-ba83-47bb-a347-6ea9d7eb3997/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862115.1_ASM1686211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:30:43,144] [INFO] Task succeeded: Blastn
[2024-01-25 20:30:43,151] [INFO] Selected 17 target genomes.
[2024-01-25 20:30:43,151] [INFO] Target genome list was writen to GCF_016862115.1_ASM1686211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:30:43,192] [INFO] Task started: fastANI
[2024-01-25 20:30:43,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af02191-78f1-4b6d-8f0c-02c4aaeaf857/GCF_016862115.1_ASM1686211v1_genomic.fna.gz --refList GCF_016862115.1_ASM1686211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862115.1_ASM1686211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:31:24,372] [INFO] Task succeeded: fastANI
[2024-01-25 20:31:24,382] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:31:24,383] [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_016862115.1	s__Actinoplanes deccanensis	100.0	3414	3430	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_900215205.1	s__Actinoplanes atraurantiacus	87.136	2584	3430	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	83.2942	2015	3430	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	83.1056	2021	3430	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	83.1026	1921	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014204895.1	s__Actinoplanes abujensis	83.0155	1972	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016834655.1	s__Actinoplanes sp016834655	82.9295	2083	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	82.7072	1959	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332695.1	s__Actinoplanes toevensis	82.2276	1905	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862435.1	s__Actinoplanes tereljensis	81.9817	1933	3430	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	81.9624	1823	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	80.9587	1529	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	80.8615	1812	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012911935.1	s__Pseudonocardia sp012911935	76.0824	753	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187395.1	s__Kytococcus aerolatus	76.0382	284	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kytococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620785.1	s__Pseudonocardia acaciae	75.7717	1022	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882645.1	s__Chersky-822 sp017882645	75.4888	366	3430	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Chersky-822	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:31:24,384] [INFO] GTDB search result was written to GCF_016862115.1_ASM1686211v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:31:24,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:31:24,387] [INFO] DFAST_QC result json was written to GCF_016862115.1_ASM1686211v1_genomic.fna/dqc_result.json
[2024-01-25 20:31:24,388] [INFO] DFAST_QC completed!
[2024-01-25 20:31:24,388] [INFO] Total running time: 0h4m4s