[2024-01-24 12:06:11,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference
[2024-01-24 12:06:13,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,246] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa7062af-1328-45bf-a10c-ea822af093de/GCF_016918035.1_ASM1691803v1_genomic.fna.gz | prodigal -d GCF_016918035.1_ASM1691803v1_genomic.fna/cds.fna -a GCF_016918035.1_ASM1691803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,902] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,902] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,903] [INFO] Running command: hmmsearch --tblout GCF_016918035.1_ASM1691803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/reference_markers.hmm GCF_016918035.1_ASM1691803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:27,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:27,222] [INFO] Found 6/6 markers.
[2024-01-24 12:06:27,273] [INFO] Query marker FASTA was written to GCF_016918035.1_ASM1691803v1_genomic.fna/markers.fasta
[2024-01-24 12:06:27,274] [INFO] Task started: Blastn
[2024-01-24 12:06:27,274] [INFO] Running command: blastn -query GCF_016918035.1_ASM1691803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/reference_markers.fasta -out GCF_016918035.1_ASM1691803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:28,536] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:28,540] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:28,540] [INFO] Target genome list was writen to GCF_016918035.1_ASM1691803v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:28,546] [INFO] Task started: fastANI
[2024-01-24 12:06:28,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7062af-1328-45bf-a10c-ea822af093de/GCF_016918035.1_ASM1691803v1_genomic.fna.gz --refList GCF_016918035.1_ASM1691803v1_genomic.fna/target_genomes.txt --output GCF_016918035.1_ASM1691803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:48,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:48,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:48,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:48,724] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:48,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:48,725] [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 leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	100.0	1469	1470	95	conclusive
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	79.7091	658	1470	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	79.2358	652	1470	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	79.1203	629	1470	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	78.8767	631	1470	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.3666	577	1470	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	77.8749	480	1470	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	77.1695	450	1470	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	77.059	481	1470	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	77.0542	485	1470	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	76.9057	476	1470	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	76.7767	491	1470	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	76.7213	474	1470	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	76.516	465	1470	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	76.4014	271	1470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:48,727] [INFO] DFAST Taxonomy check result was written to GCF_016918035.1_ASM1691803v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:48,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:48,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:48,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/checkm_data
[2024-01-24 12:06:48,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:48,772] [INFO] Task started: CheckM
[2024-01-24 12:06:48,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918035.1_ASM1691803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918035.1_ASM1691803v1_genomic.fna/checkm_input GCF_016918035.1_ASM1691803v1_genomic.fna/checkm_result
[2024-01-24 12:08:07,395] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:07,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:07,419] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:07,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:07,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918035.1_ASM1691803v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:07,420] [INFO] Task started: Blastn
[2024-01-24 12:08:07,420] [INFO] Running command: blastn -query GCF_016918035.1_ASM1691803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd274a69e-581f-43ce-8380-3a7026b01885/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918035.1_ASM1691803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:09,258] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:09,263] [INFO] Selected 14 target genomes.
[2024-01-24 12:08:09,264] [INFO] Target genome list was writen to GCF_016918035.1_ASM1691803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:09,277] [INFO] Task started: fastANI
[2024-01-24 12:08:09,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7062af-1328-45bf-a10c-ea822af093de/GCF_016918035.1_ASM1691803v1_genomic.fna.gz --refList GCF_016918035.1_ASM1691803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918035.1_ASM1691803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:24,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:24,382] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:24,382] [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_016918035.1	s__Nakamurella sp016918035	100.0	1469	1470	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_016918095.1	s__Nakamurella flavida	79.7378	655	1470	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	79.2167	653	1470	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	79.1137	630	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707545.1	s__Nakamurella sp009707545	78.8915	648	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646215.1	s__Nakamurella endophytica	78.835	637	1470	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	78.3652	577	1470	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	78.302	464	1470	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	78.1793	427	1470	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	77.8941	403	1470	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	77.8408	384	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	77.1631	449	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994135.1	s__Modestobacter roseus	76.9336	472	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_014208095.1	s__Pseudonocardia eucalypti	76.9252	534	1470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:24,384] [INFO] GTDB search result was written to GCF_016918035.1_ASM1691803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:24,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:24,388] [INFO] DFAST_QC result json was written to GCF_016918035.1_ASM1691803v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:24,388] [INFO] DFAST_QC completed!
[2024-01-24 12:08:24,388] [INFO] Total running time: 0h2m13s