[2024-01-25 17:51:05,478] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:05,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:05,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference
[2024-01-25 17:51:06,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:06,565] [INFO] Task started: Prodigal
[2024-01-25 17:51:06,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6e03c5e-86db-47f2-9d26-727b9844f83c/GCF_000423625.1_ASM42362v1_genomic.fna.gz | prodigal -d GCF_000423625.1_ASM42362v1_genomic.fna/cds.fna -a GCF_000423625.1_ASM42362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:18,834] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:18,834] [INFO] Task started: HMMsearch
[2024-01-25 17:51:18,834] [INFO] Running command: hmmsearch --tblout GCF_000423625.1_ASM42362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/reference_markers.hmm GCF_000423625.1_ASM42362v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:19,089] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:19,090] [INFO] Found 6/6 markers.
[2024-01-25 17:51:19,134] [INFO] Query marker FASTA was written to GCF_000423625.1_ASM42362v1_genomic.fna/markers.fasta
[2024-01-25 17:51:19,134] [INFO] Task started: Blastn
[2024-01-25 17:51:19,134] [INFO] Running command: blastn -query GCF_000423625.1_ASM42362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/reference_markers.fasta -out GCF_000423625.1_ASM42362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:20,291] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:20,299] [INFO] Selected 15 target genomes.
[2024-01-25 17:51:20,300] [INFO] Target genome list was writen to GCF_000423625.1_ASM42362v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:20,327] [INFO] Task started: fastANI
[2024-01-25 17:51:20,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e03c5e-86db-47f2-9d26-727b9844f83c/GCF_000423625.1_ASM42362v1_genomic.fna.gz --refList GCF_000423625.1_ASM42362v1_genomic.fna/target_genomes.txt --output GCF_000423625.1_ASM42362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:40,342] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:40,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:40,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:40,352] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:40,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:40,352] [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
Pseudonocardia asaccharolytica	strain=DSM 44247	GCA_000423625.1	54010	54010	type	True	100.0	1642	1645	95	conclusive
Pseudonocardia asaccharolytica	strain=NBRC 16224	GCA_007989065.1	54010	54010	type	True	99.9328	1571	1645	95	conclusive
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	81.6823	878	1645	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	81.6547	956	1645	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	80.2601	902	1645	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.9888	862	1645	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	79.9884	839	1645	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	79.6388	893	1645	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	79.5632	848	1645	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	79.2543	829	1645	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	76.2922	353	1645	95	below_threshold
Tersicoccus phoenicis	strain=DSM 30849	GCA_001968835.1	554083	554083	type	True	76.2423	197	1645	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	76.1116	163	1645	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_014639315.1	1774748	1774748	type	True	76.0755	162	1645	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	75.986	373	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:40,366] [INFO] DFAST Taxonomy check result was written to GCF_000423625.1_ASM42362v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:40,367] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:40,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:40,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/checkm_data
[2024-01-25 17:51:40,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:40,417] [INFO] Task started: CheckM
[2024-01-25 17:51:40,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423625.1_ASM42362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423625.1_ASM42362v1_genomic.fna/checkm_input GCF_000423625.1_ASM42362v1_genomic.fna/checkm_result
[2024-01-25 17:52:25,778] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:25,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:25,798] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:25,798] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:25,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423625.1_ASM42362v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:25,799] [INFO] Task started: Blastn
[2024-01-25 17:52:25,799] [INFO] Running command: blastn -query GCF_000423625.1_ASM42362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2119f284-f416-433b-9656-6ff112291446/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423625.1_ASM42362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:27,572] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:27,575] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:27,575] [INFO] Target genome list was writen to GCF_000423625.1_ASM42362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:27,588] [INFO] Task started: fastANI
[2024-01-25 17:52:27,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e03c5e-86db-47f2-9d26-727b9844f83c/GCF_000423625.1_ASM42362v1_genomic.fna.gz --refList GCF_000423625.1_ASM42362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423625.1_ASM42362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:47,806] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:47,815] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:47,816] [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_000423625.1	s__Pseudonocardia asaccharolytica	100.0	1642	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_012911875.1	s__Pseudonocardia bannensis	81.6713	878	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911935.1	s__Pseudonocardia sp012911935	81.6673	955	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531475.1	s__Pseudonocardia sp018531475	81.4895	935	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	80.2976	897	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	79.9925	838	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531445.1	s__Pseudonocardia sp018531445	79.7079	827	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	79.5815	905	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	79.5112	858	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942185.1	s__Pseudonocardia sp001942185	79.3897	862	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142365.1	s__Pseudonocardia thermophila	79.2271	775	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968835.1	s__Tersicoccus phoenicis	76.2019	202	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968825.1	s__Tersicoccus sp001968825	76.1387	225	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639315.1	s__Sediminivirga luteola	76.0768	162	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Sediminivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	75.9591	380	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:47,817] [INFO] GTDB search result was written to GCF_000423625.1_ASM42362v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:47,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:47,821] [INFO] DFAST_QC result json was written to GCF_000423625.1_ASM42362v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:47,821] [INFO] DFAST_QC completed!
[2024-01-25 17:52:47,821] [INFO] Total running time: 0h1m42s