[2024-01-25 20:27:35,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:35,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:35,627] [INFO] DQC Reference Directory: /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference
[2024-01-25 20:27:36,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:36,771] [INFO] Task started: Prodigal
[2024-01-25 20:27:36,771] [INFO] Running command: gunzip -c /var/lib/cwl/stge6358164-7927-4ac0-8747-555e148e5768/GCF_015674855.1_ASM1567485v1_genomic.fna.gz | prodigal -d GCF_015674855.1_ASM1567485v1_genomic.fna/cds.fna -a GCF_015674855.1_ASM1567485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:28:16,520] [INFO] Task succeeded: Prodigal
[2024-01-25 20:28:16,521] [INFO] Task started: HMMsearch
[2024-01-25 20:28:16,521] [INFO] Running command: hmmsearch --tblout GCF_015674855.1_ASM1567485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/reference_markers.hmm GCF_015674855.1_ASM1567485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:28:16,845] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:28:16,847] [INFO] Found 6/6 markers.
[2024-01-25 20:28:16,910] [INFO] Query marker FASTA was written to GCF_015674855.1_ASM1567485v1_genomic.fna/markers.fasta
[2024-01-25 20:28:16,911] [INFO] Task started: Blastn
[2024-01-25 20:28:16,911] [INFO] Running command: blastn -query GCF_015674855.1_ASM1567485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/reference_markers.fasta -out GCF_015674855.1_ASM1567485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:18,056] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:18,059] [INFO] Selected 12 target genomes.
[2024-01-25 20:28:18,059] [INFO] Target genome list was writen to GCF_015674855.1_ASM1567485v1_genomic.fna/target_genomes.txt
[2024-01-25 20:28:18,076] [INFO] Task started: fastANI
[2024-01-25 20:28:18,076] [INFO] Running command: fastANI --query /var/lib/cwl/stge6358164-7927-4ac0-8747-555e148e5768/GCF_015674855.1_ASM1567485v1_genomic.fna.gz --refList GCF_015674855.1_ASM1567485v1_genomic.fna/target_genomes.txt --output GCF_015674855.1_ASM1567485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:41,624] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:41,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:41,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:41,633] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:41,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:41,634] [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
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	100.0	2745	2752	95	conclusive
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	84.4248	1528	2752	95	below_threshold
Nocardia arizonensis	strain=NBRC 108935	GCA_001618405.1	1141647	1141647	type	True	84.3689	1529	2752	95	below_threshold
Nocardia takedensis	strain=NBRC 100417	GCA_000308695.1	259390	259390	type	True	83.6098	1562	2752	95	below_threshold
Nocardia noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	82.5748	1532	2752	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.8589	1316	2752	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.8194	1321	2752	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	81.819	1299	2752	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.677	1290	2752	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	80.9562	1181	2752	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	80.5866	1126	2752	95	below_threshold
Nocardia aurantia	strain=RB56	GCA_009604425.1	2585199	2585199	type	True	79.1698	1120	2752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:41,636] [INFO] DFAST Taxonomy check result was written to GCF_015674855.1_ASM1567485v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:41,636] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:41,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:41,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/checkm_data
[2024-01-25 20:28:41,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:41,712] [INFO] Task started: CheckM
[2024-01-25 20:28:41,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015674855.1_ASM1567485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015674855.1_ASM1567485v1_genomic.fna/checkm_input GCF_015674855.1_ASM1567485v1_genomic.fna/checkm_result
[2024-01-25 20:30:36,973] [INFO] Task succeeded: CheckM
[2024-01-25 20:30:36,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:30:36,999] [INFO] ===== Completeness check finished =====
[2024-01-25 20:30:36,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:30:37,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015674855.1_ASM1567485v1_genomic.fna/markers.fasta)
[2024-01-25 20:30:37,000] [INFO] Task started: Blastn
[2024-01-25 20:30:37,000] [INFO] Running command: blastn -query GCF_015674855.1_ASM1567485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2b5a29a-5202-4c90-bd91-14d0b54bd4d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_015674855.1_ASM1567485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:30:38,762] [INFO] Task succeeded: Blastn
[2024-01-25 20:30:38,766] [INFO] Selected 14 target genomes.
[2024-01-25 20:30:38,766] [INFO] Target genome list was writen to GCF_015674855.1_ASM1567485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:30:38,799] [INFO] Task started: fastANI
[2024-01-25 20:30:38,800] [INFO] Running command: fastANI --query /var/lib/cwl/stge6358164-7927-4ac0-8747-555e148e5768/GCF_015674855.1_ASM1567485v1_genomic.fna.gz --refList GCF_015674855.1_ASM1567485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015674855.1_ASM1567485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:31:06,818] [INFO] Task succeeded: fastANI
[2024-01-25 20:31:06,827] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:31:06,827] [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_015674855.1	s__Nocardia bovistercoris	100.0	2745	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001310275.1	s__Nocardia arizonensis	84.3961	1533	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000308695.1	s__Nocardia takedensis	83.6134	1561	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123685.1	s__Nocardia aurea	82.374	1671	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	-
GCF_001612615.1	s__Nocardia amikacinitolerans	81.8627	1317	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	81.783	1302	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	81.695	1281	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	81.6726	1290	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315035.1	s__Nocardia puris	81.4605	1294	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_001612985.1	s__Nocardia gamkensis	81.0886	1251	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_001612765.1	s__Nocardia arthritidis	80.9894	1193	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	80.5681	1130	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801145.1	s__Nocardia arthritidis_A	80.3795	1219	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381925.1	s__Nocardia sp000381925	79.2949	1114	2752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:31:06,829] [INFO] GTDB search result was written to GCF_015674855.1_ASM1567485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:31:06,830] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:31:06,834] [INFO] DFAST_QC result json was written to GCF_015674855.1_ASM1567485v1_genomic.fna/dqc_result.json
[2024-01-25 20:31:06,834] [INFO] DFAST_QC completed!
[2024-01-25 20:31:06,834] [INFO] Total running time: 0h3m31s