[2024-01-24 13:40:45,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,882] [INFO] DQC Reference Directory: /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference
[2024-01-24 13:40:47,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,206] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgad7763c4-fe1d-4ffa-9e4f-27ba4983db3b/GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna.gz | prodigal -d GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/cds.fna -a GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:04,260] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:04,260] [INFO] Task started: HMMsearch
[2024-01-24 13:41:04,260] [INFO] Running command: hmmsearch --tblout GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/reference_markers.hmm GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:04,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:04,559] [INFO] Found 6/6 markers.
[2024-01-24 13:41:04,602] [INFO] Query marker FASTA was written to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta
[2024-01-24 13:41:04,602] [INFO] Task started: Blastn
[2024-01-24 13:41:04,603] [INFO] Running command: blastn -query GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/reference_markers.fasta -out GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:05,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:05,729] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:05,730] [INFO] Target genome list was writen to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt
[2024-01-24 13:41:05,793] [INFO] Task started: fastANI
[2024-01-24 13:41:05,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7763c4-fe1d-4ffa-9e4f-27ba4983db3b/GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt --output GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:25,008] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:25,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:25,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:25,025] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:25,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:25,026] [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
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	100.0	1725	1727	95	conclusive
Nocardiopsis xinjiangensis	strain=YIM 90004	GCA_000341145.1	124285	124285	type	True	91.0453	1420	1727	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	86.8363	1323	1727	95	below_threshold
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	86.2524	1226	1727	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	81.7561	1028	1727	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	81.7364	1051	1727	95	below_threshold
Nocardiopsis quinghaiensis	strain=YIM 28A4	GCA_008638365.1	464995	464995	type	True	81.7297	992	1727	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	81.7254	945	1727	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	81.4933	1029	1727	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	81.296	997	1727	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	81.2656	941	1727	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	81.2542	770	1727	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	80.8181	855	1727	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.0359	543	1727	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	78.9483	618	1727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:25,027] [INFO] DFAST Taxonomy check result was written to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/tc_result.tsv
[2024-01-24 13:41:25,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:25,028] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:25,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/checkm_data
[2024-01-24 13:41:25,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:25,080] [INFO] Task started: CheckM
[2024-01-24 13:41:25,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/checkm_input GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/checkm_result
[2024-01-24 13:42:23,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:23,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:23,884] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:23,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:23,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta)
[2024-01-24 13:42:23,885] [INFO] Task started: Blastn
[2024-01-24 13:42:23,885] [INFO] Running command: blastn -query GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stgba72094d-1bdd-4a84-ae98-a226c302261c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:25,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:25,531] [INFO] Selected 11 target genomes.
[2024-01-24 13:42:25,531] [INFO] Target genome list was writen to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:25,580] [INFO] Task started: fastANI
[2024-01-24 13:42:25,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7763c4-fe1d-4ffa-9e4f-27ba4983db3b/GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt --output GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:39,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:39,364] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:39,364] [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_000340965.1	s__Nocardiopsis kunsanensis	100.0	1725	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.42	99.42	0.93	0.93	2	conclusive
GCF_000341145.1	s__Nocardiopsis xinjiangensis	91.0669	1418	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892575.1	s__Nocardiopsis coralli	86.8142	1326	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341025.1	s__Nocardiopsis salina	86.2701	1224	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396365.1	s__Nocardiopsis alborubida	81.7709	1046	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_000341065.1	s__Nocardiopsis halotolerans	81.7048	948	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	81.6908	994	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCA_002529455.1	s__Nocardiopsis fusca	81.6798	1057	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341265.1	s__Nocardiopsis prasina	81.2746	939	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCF_000515115.1	s__Nocardiopsis sp000515115	81.0977	781	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341005.1	s__Nocardiopsis alkaliphila	80.8155	855	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:39,366] [INFO] GTDB search result was written to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:39,367] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:39,371] [INFO] DFAST_QC result json was written to GCF_000340965.1_SOAPdenovo_v1.06_genomic.fna/dqc_result.json
[2024-01-24 13:42:39,371] [INFO] DFAST_QC completed!
[2024-01-24 13:42:39,371] [INFO] Total running time: 0h1m54s