[2024-01-24 13:26:14,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:14,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:14,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference
[2024-01-24 13:26:15,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:15,560] [INFO] Task started: Prodigal
[2024-01-24 13:26:15,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb43192c-ea0f-42ee-b1ce-3679c40dab10/GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/cds.fna -a GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:43,156] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:43,157] [INFO] Task started: HMMsearch
[2024-01-24 13:26:43,157] [INFO] Running command: hmmsearch --tblout GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/reference_markers.hmm GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:43,563] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:43,565] [INFO] Found 6/6 markers.
[2024-01-24 13:26:43,641] [INFO] Query marker FASTA was written to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:26:43,641] [INFO] Task started: Blastn
[2024-01-24 13:26:43,641] [INFO] Running command: blastn -query GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/reference_markers.fasta -out GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:44,871] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:44,877] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:44,878] [INFO] Target genome list was writen to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:26:44,880] [INFO] Task started: fastANI
[2024-01-24 13:26:44,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb43192c-ea0f-42ee-b1ce-3679c40dab10/GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna.gz --refList GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:13,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:13,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:13,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:13,146] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:27:13,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:13,147] [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 regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	100.0	3300	3302	95	conclusive
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	99.9699	3205	3302	95	conclusive
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	85.8263	1757	3302	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	85.7542	1847	3302	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	85.7371	2054	3302	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	85.7278	1848	3302	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	85.7002	2112	3302	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	85.652	2090	3302	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.6836	1832	3302	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.14	843	3302	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.0318	928	3302	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.9923	1122	3302	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.8373	1080	3302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:13,149] [INFO] DFAST Taxonomy check result was written to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:27:13,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:13,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:13,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/checkm_data
[2024-01-24 13:27:13,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:13,241] [INFO] Task started: CheckM
[2024-01-24 13:27:13,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/checkm_input GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:28:38,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:38,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:38,067] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:38,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:38,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:28:38,068] [INFO] Task started: Blastn
[2024-01-24 13:28:38,068] [INFO] Running command: blastn -query GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg612b34a9-4426-41e7-859c-f0026125f6ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:39,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:39,920] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:39,921] [INFO] Target genome list was writen to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:39,936] [INFO] Task started: fastANI
[2024-01-24 13:28:39,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb43192c-ea0f-42ee-b1ce-3679c40dab10/GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna.gz --refList GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:05,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,734] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:05,734] [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_900188005.1	s__Actinoplanes regularis	100.0	3300	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016862395.1	s__Actinoplanes siamensis	86.1233	1850	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	85.7276	1849	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_014205225.1	s__Actinoplanes octamycinicus	85.6831	2114	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	85.6419	2094	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000715855.1	s__Actinoplanes liguriensis	85.4481	2168	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	85.4446	2135	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_016862095.1	s__Actinoplanes cyaneus	85.254	2116	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	84.7706	1935	3302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,736] [INFO] GTDB search result was written to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:05,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:05,739] [INFO] DFAST_QC result json was written to GCF_900188005.1_IMG-taxon_2724679777_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:29:05,739] [INFO] DFAST_QC completed!
[2024-01-24 13:29:05,740] [INFO] Total running time: 0h2m51s