[2024-01-24 13:31:12,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference
[2024-01-24 13:31:13,561] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,562] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,562] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1043735-c90f-4ce6-a044-b471b0f9fb93/GCF_014892575.1_ASM1489257v1_genomic.fna.gz | prodigal -d GCF_014892575.1_ASM1489257v1_genomic.fna/cds.fna -a GCF_014892575.1_ASM1489257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:32,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:32,012] [INFO] Task started: HMMsearch
[2024-01-24 13:31:32,012] [INFO] Running command: hmmsearch --tblout GCF_014892575.1_ASM1489257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/reference_markers.hmm GCF_014892575.1_ASM1489257v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:32,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:32,279] [INFO] Found 6/6 markers.
[2024-01-24 13:31:32,331] [INFO] Query marker FASTA was written to GCF_014892575.1_ASM1489257v1_genomic.fna/markers.fasta
[2024-01-24 13:31:32,331] [INFO] Task started: Blastn
[2024-01-24 13:31:32,331] [INFO] Running command: blastn -query GCF_014892575.1_ASM1489257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/reference_markers.fasta -out GCF_014892575.1_ASM1489257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:33,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:33,524] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:33,524] [INFO] Target genome list was writen to GCF_014892575.1_ASM1489257v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:33,528] [INFO] Task started: fastANI
[2024-01-24 13:31:33,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1043735-c90f-4ce6-a044-b471b0f9fb93/GCF_014892575.1_ASM1489257v1_genomic.fna.gz --refList GCF_014892575.1_ASM1489257v1_genomic.fna/target_genomes.txt --output GCF_014892575.1_ASM1489257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:57,621] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:57,622] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:57,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:57,639] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:57,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:57,640] [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 coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	100.0	2100	2103	95	conclusive
Nocardiopsis salina	strain=YIM 90010	GCA_000341025.1	245836	245836	type	True	92.3286	1518	2103	95	below_threshold
Nocardiopsis xinjiangensis	strain=YIM 90004	GCA_000341145.1	124285	124285	type	True	87.2552	1369	2103	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	86.8521	1317	2103	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	82.6198	999	2103	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	82.4899	1170	2103	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	82.2597	1156	2103	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	82.2164	1190	2103	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	82.0159	1141	2103	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	81.9347	862	2103	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	81.8963	1038	2103	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	81.5346	1173	2103	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	81.2026	916	2103	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	79.5711	771	2103	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	79.4661	882	2103	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.1401	760	2103	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.005	684	2103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:57,644] [INFO] DFAST Taxonomy check result was written to GCF_014892575.1_ASM1489257v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:57,644] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:57,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:57,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/checkm_data
[2024-01-24 13:31:57,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:57,714] [INFO] Task started: CheckM
[2024-01-24 13:31:57,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014892575.1_ASM1489257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014892575.1_ASM1489257v1_genomic.fna/checkm_input GCF_014892575.1_ASM1489257v1_genomic.fna/checkm_result
[2024-01-24 13:33:41,258] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:41,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:41,279] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:41,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:41,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014892575.1_ASM1489257v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:41,280] [INFO] Task started: Blastn
[2024-01-24 13:33:41,280] [INFO] Running command: blastn -query GCF_014892575.1_ASM1489257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55bc4c15-0cc6-4186-9e83-465ddd3e0063/dqc_reference/reference_markers_gtdb.fasta -out GCF_014892575.1_ASM1489257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:43,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:43,110] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:43,110] [INFO] Target genome list was writen to GCF_014892575.1_ASM1489257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:43,124] [INFO] Task started: fastANI
[2024-01-24 13:33:43,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1043735-c90f-4ce6-a044-b471b0f9fb93/GCF_014892575.1_ASM1489257v1_genomic.fna.gz --refList GCF_014892575.1_ASM1489257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014892575.1_ASM1489257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:02,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:02,287] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:02,287] [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_014892575.1	s__Nocardiopsis coralli	100.0	2100	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000341025.1	s__Nocardiopsis salina	92.3178	1521	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341145.1	s__Nocardiopsis xinjiangensis	87.2494	1370	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340965.1	s__Nocardiopsis kunsanensis	86.8601	1316	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.42	99.42	0.93	0.93	2	-
GCA_002529455.1	s__Nocardiopsis fusca	82.5098	1153	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905145.1	s__Nocardiopsis sp001905145	82.4049	1130	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	82.049	1116	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	82.0041	1143	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	81.933	1193	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	81.9237	863	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570765.1	s__Nocardiopsis listeri	81.9042	1037	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515115.1	s__Nocardiopsis sp000515115	81.5875	881	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141985.1	s__Nocardiopsis flavescens	81.5267	1176	2103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115445.1	s__Nocardiopsis merdipullorum	80.8271	685	2103	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 13:34:02,289] [INFO] GTDB search result was written to GCF_014892575.1_ASM1489257v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:02,289] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:02,293] [INFO] DFAST_QC result json was written to GCF_014892575.1_ASM1489257v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:02,293] [INFO] DFAST_QC completed!
[2024-01-24 13:34:02,293] [INFO] Total running time: 0h2m50s