[2024-01-25 20:06:35,505] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:35,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:35,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference
[2024-01-25 20:06:36,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:36,649] [INFO] Task started: Prodigal
[2024-01-25 20:06:36,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a5e6892-5388-4690-af8c-eb5eabb505f0/GCF_009707545.1_ASM970754v1_genomic.fna.gz | prodigal -d GCF_009707545.1_ASM970754v1_genomic.fna/cds.fna -a GCF_009707545.1_ASM970754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:55,762] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:55,762] [INFO] Task started: HMMsearch
[2024-01-25 20:06:55,762] [INFO] Running command: hmmsearch --tblout GCF_009707545.1_ASM970754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/reference_markers.hmm GCF_009707545.1_ASM970754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:56,066] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:56,067] [INFO] Found 6/6 markers.
[2024-01-25 20:06:56,116] [INFO] Query marker FASTA was written to GCF_009707545.1_ASM970754v1_genomic.fna/markers.fasta
[2024-01-25 20:06:56,116] [INFO] Task started: Blastn
[2024-01-25 20:06:56,116] [INFO] Running command: blastn -query GCF_009707545.1_ASM970754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/reference_markers.fasta -out GCF_009707545.1_ASM970754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:57,309] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:57,311] [INFO] Selected 18 target genomes.
[2024-01-25 20:06:57,312] [INFO] Target genome list was writen to GCF_009707545.1_ASM970754v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:57,333] [INFO] Task started: fastANI
[2024-01-25 20:06:57,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5e6892-5388-4690-af8c-eb5eabb505f0/GCF_009707545.1_ASM970754v1_genomic.fna.gz --refList GCF_009707545.1_ASM970754v1_genomic.fna/target_genomes.txt --output GCF_009707545.1_ASM970754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:18,123] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:18,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:18,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:18,134] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:07:18,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:07:18,135] [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
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	79.6311	791	2004	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	79.0396	615	2004	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	78.9607	627	2004	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	78.8002	643	2004	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	78.7359	708	2004	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.6632	631	2004	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	78.4799	563	2004	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	77.4091	419	2004	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	76.9479	579	2004	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.9353	480	2004	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	76.8315	595	2004	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	76.7477	641	2004	95	below_threshold
Cellulomonas taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	76.5781	376	2004	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.4397	656	2004	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	76.3801	562	2004	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	76.3683	321	2004	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.1595	353	2004	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	76.0291	361	2004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:18,136] [INFO] DFAST Taxonomy check result was written to GCF_009707545.1_ASM970754v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:18,136] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:18,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:18,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/checkm_data
[2024-01-25 20:07:18,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:18,206] [INFO] Task started: CheckM
[2024-01-25 20:07:18,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707545.1_ASM970754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707545.1_ASM970754v1_genomic.fna/checkm_input GCF_009707545.1_ASM970754v1_genomic.fna/checkm_result
[2024-01-25 20:09:55,904] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:55,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:55,923] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:55,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:55,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707545.1_ASM970754v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:55,924] [INFO] Task started: Blastn
[2024-01-25 20:09:55,924] [INFO] Running command: blastn -query GCF_009707545.1_ASM970754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672d434b-ddf6-47e9-ae28-3de4df264a13/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707545.1_ASM970754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:57,687] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:57,690] [INFO] Selected 16 target genomes.
[2024-01-25 20:09:57,690] [INFO] Target genome list was writen to GCF_009707545.1_ASM970754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:57,723] [INFO] Task started: fastANI
[2024-01-25 20:09:57,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5e6892-5388-4690-af8c-eb5eabb505f0/GCF_009707545.1_ASM970754v1_genomic.fna.gz --refList GCF_009707545.1_ASM970754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707545.1_ASM970754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:10:15,217] [INFO] Task succeeded: fastANI
[2024-01-25 20:10:15,229] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:10:15,229] [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_009707545.1	s__Nakamurella sp009707545	100.0	2002	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646215.1	s__Nakamurella endophytica	79.668	785	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918035.1	s__Nakamurella sp016918035	79.0446	612	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104535.1	s__Nakamurella panacisegetis	79.0201	621	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918095.1	s__Nakamurella flavida	78.9697	624	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298075.1	s__Nakamurella flava	78.793	644	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024365.1	s__Nakamurella multipartita	78.7647	705	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260015.1	s__Nakamurella deserti	78.6899	627	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014303395.1	s__Nakamurella sp014303395	78.6777	600	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426645.1	s__Nakamurella lactea	78.5106	559	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576535.1	s__Nakamurella silvestris	78.182	505	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882715.1	s__Nakamurella sp017882715	77.9462	392	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204915.1	s__Crossiella cryophila	76.7722	634	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931845.1	s__Cellulomonas taurus	76.5797	375	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339565.1	s__Pseudonocardia endophytica	76.3868	560	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	76.1383	359	2004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:10:15,231] [INFO] GTDB search result was written to GCF_009707545.1_ASM970754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:10:15,231] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:10:15,234] [INFO] DFAST_QC result json was written to GCF_009707545.1_ASM970754v1_genomic.fna/dqc_result.json
[2024-01-25 20:10:15,234] [INFO] DFAST_QC completed!
[2024-01-25 20:10:15,234] [INFO] Total running time: 0h3m40s