[2024-01-24 10:47:24,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,487] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference
[2024-01-24 10:47:26,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,475] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg7eb04329-161b-4893-9ebf-9b957f9c62b4/GCF_024539675.1_ASM2453967v1_genomic.fna.gz | prodigal -d GCF_024539675.1_ASM2453967v1_genomic.fna/cds.fna -a GCF_024539675.1_ASM2453967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:48,931] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:48,932] [INFO] Task started: HMMsearch
[2024-01-24 10:47:48,932] [INFO] Running command: hmmsearch --tblout GCF_024539675.1_ASM2453967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/reference_markers.hmm GCF_024539675.1_ASM2453967v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:49,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:49,299] [INFO] Found 6/6 markers.
[2024-01-24 10:47:49,371] [INFO] Query marker FASTA was written to GCF_024539675.1_ASM2453967v1_genomic.fna/markers.fasta
[2024-01-24 10:47:49,372] [INFO] Task started: Blastn
[2024-01-24 10:47:49,372] [INFO] Running command: blastn -query GCF_024539675.1_ASM2453967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/reference_markers.fasta -out GCF_024539675.1_ASM2453967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,676] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,680] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:50,681] [INFO] Target genome list was writen to GCF_024539675.1_ASM2453967v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:50,689] [INFO] Task started: fastANI
[2024-01-24 10:47:50,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb04329-161b-4893-9ebf-9b957f9c62b4/GCF_024539675.1_ASM2453967v1_genomic.fna.gz --refList GCF_024539675.1_ASM2453967v1_genomic.fna/target_genomes.txt --output GCF_024539675.1_ASM2453967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:30,107] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:30,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:30,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:30,124] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:30,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:30,124] [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
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	92.3159	2188	2774	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	91.4933	2055	2774	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	88.0538	2076	2774	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	88.0307	2048	2774	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	86.7967	1972	2774	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.538	1639	2774	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	86.535	1973	2774	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9484	1805	2774	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.9416	1727	2774	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.5905	1643	2774	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.3611	1664	2774	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	84.2654	1780	2774	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.1606	1705	2774	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.6514	1758	2774	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	83.5497	1713	2774	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.4418	1795	2774	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.2701	1732	2774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:30,127] [INFO] DFAST Taxonomy check result was written to GCF_024539675.1_ASM2453967v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:30,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:30,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:30,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/checkm_data
[2024-01-24 10:48:30,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:30,219] [INFO] Task started: CheckM
[2024-01-24 10:48:30,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024539675.1_ASM2453967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024539675.1_ASM2453967v1_genomic.fna/checkm_input GCF_024539675.1_ASM2453967v1_genomic.fna/checkm_result
[2024-01-24 10:49:44,166] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:44,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.42%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:44,498] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:44,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:44,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024539675.1_ASM2453967v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:44,499] [INFO] Task started: Blastn
[2024-01-24 10:49:44,499] [INFO] Running command: blastn -query GCF_024539675.1_ASM2453967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86e86f4c-2b08-4c44-9900-6c2262278640/dqc_reference/reference_markers_gtdb.fasta -out GCF_024539675.1_ASM2453967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:46,591] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:46,595] [INFO] Selected 12 target genomes.
[2024-01-24 10:49:46,595] [INFO] Target genome list was writen to GCF_024539675.1_ASM2453967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:46,619] [INFO] Task started: fastANI
[2024-01-24 10:49:46,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb04329-161b-4893-9ebf-9b957f9c62b4/GCF_024539675.1_ASM2453967v1_genomic.fna.gz --refList GCF_024539675.1_ASM2453967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024539675.1_ASM2453967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:15,482] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:15,498] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:15,498] [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_003112535.1	s__Streptomyces rishiriensis	92.294	2191	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746365.1	s__Streptomyces sp001746365	92.1473	2201	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649655.1	s__Streptomyces humidus	91.4809	2056	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001298545.1	s__Streptomyces sp001298545	88.428	2070	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.23	95.13	0.87	0.84	4	-
GCF_900129855.1	s__Streptomyces sp900129855	88.417	1980	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_001184025.1	s__Streptomyces sp001184025	88.4166	1936	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	98.49	0.84	0.84	2	-
GCF_001428885.1	s__Streptomyces sp001428885	88.1182	2060	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860545.1	s__Streptomyces asoensis	88.0667	2075	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
GCF_900110755.1	s__Streptomyces sp900110755	88.0423	1878	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003032475.1	s__Streptomyces sp003032475	87.8303	2002	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648915.1	s__Streptomyces phaeofaciens	86.7645	1977	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	83.5118	1680	2774	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:15,500] [INFO] GTDB search result was written to GCF_024539675.1_ASM2453967v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:15,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:15,504] [INFO] DFAST_QC result json was written to GCF_024539675.1_ASM2453967v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:15,504] [INFO] DFAST_QC completed!
[2024-01-24 10:50:15,504] [INFO] Total running time: 0h2m51s