[2024-01-24 13:17:32,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:32,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:32,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference
[2024-01-24 13:17:34,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:34,222] [INFO] Task started: Prodigal
[2024-01-24 13:17:34,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg5da7dfeb-4b47-4f68-b3b4-61c2720c0694/GCF_017876625.1_ASM1787662v1_genomic.fna.gz | prodigal -d GCF_017876625.1_ASM1787662v1_genomic.fna/cds.fna -a GCF_017876625.1_ASM1787662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:01,716] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:01,716] [INFO] Task started: HMMsearch
[2024-01-24 13:18:01,716] [INFO] Running command: hmmsearch --tblout GCF_017876625.1_ASM1787662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/reference_markers.hmm GCF_017876625.1_ASM1787662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:02,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:02,157] [INFO] Found 6/6 markers.
[2024-01-24 13:18:02,225] [INFO] Query marker FASTA was written to GCF_017876625.1_ASM1787662v1_genomic.fna/markers.fasta
[2024-01-24 13:18:02,226] [INFO] Task started: Blastn
[2024-01-24 13:18:02,226] [INFO] Running command: blastn -query GCF_017876625.1_ASM1787662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/reference_markers.fasta -out GCF_017876625.1_ASM1787662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,706] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:03,707] [INFO] Target genome list was writen to GCF_017876625.1_ASM1787662v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:03,717] [INFO] Task started: fastANI
[2024-01-24 13:18:03,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg5da7dfeb-4b47-4f68-b3b4-61c2720c0694/GCF_017876625.1_ASM1787662v1_genomic.fna.gz --refList GCF_017876625.1_ASM1787662v1_genomic.fna/target_genomes.txt --output GCF_017876625.1_ASM1787662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:31,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:31,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:31,552] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:31,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:31,553] [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 syringium	strain=DSM 41480	GCA_017876625.1	76729	76729	type	True	100.0	2570	2571	95	conclusive
Streptomyces netropsis	strain=CECT 3265	GCA_014203545.1	55404	55404	type	True	94.3838	2171	2571	95	below_threshold
Streptomyces netropsis	strain=JCM 4063	GCA_014648835.1	55404	55404	type	True	94.383	2125	2571	95	below_threshold
Streptomyces albireticuli	strain=NRRL B-1670	GCA_002286695.1	1940	1940	type	True	85.7729	1470	2571	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.6636	1620	2571	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	85.6334	1664	2571	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.6134	1640	2571	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	85.5814	1644	2571	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	85.4631	1623	2571	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	85.4402	1620	2571	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	81.9948	1370	2571	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	81.4885	1419	2571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,555] [INFO] DFAST Taxonomy check result was written to GCF_017876625.1_ASM1787662v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:31,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:31,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:31,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/checkm_data
[2024-01-24 13:18:31,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:31,633] [INFO] Task started: CheckM
[2024-01-24 13:18:31,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876625.1_ASM1787662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876625.1_ASM1787662v1_genomic.fna/checkm_input GCF_017876625.1_ASM1787662v1_genomic.fna/checkm_result
[2024-01-24 13:20:33,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:33,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:33,793] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:33,794] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:33,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876625.1_ASM1787662v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:33,795] [INFO] Task started: Blastn
[2024-01-24 13:20:33,795] [INFO] Running command: blastn -query GCF_017876625.1_ASM1787662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd87dd7bc-8720-4784-b023-f7c3170069ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876625.1_ASM1787662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:35,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:35,908] [INFO] Selected 9 target genomes.
[2024-01-24 13:20:35,908] [INFO] Target genome list was writen to GCF_017876625.1_ASM1787662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:35,921] [INFO] Task started: fastANI
[2024-01-24 13:20:35,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg5da7dfeb-4b47-4f68-b3b4-61c2720c0694/GCF_017876625.1_ASM1787662v1_genomic.fna.gz --refList GCF_017876625.1_ASM1787662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876625.1_ASM1787662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:56,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:56,080] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:56,080] [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_017876625.1	s__Streptomyces syringium	100.0	2569	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.60	0.98	0.98	2	conclusive
GCF_014203545.1	s__Streptomyces netropsis	94.3809	2172	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018614525.1	s__Streptomyces sp018614525	86.1766	1468	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	85.9242	1585	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192455.1	s__Streptomyces albireticuli_B	85.8232	1718	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286695.1	s__Streptomyces albireticuli	85.7432	1474	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891295.1	s__Streptomyces eurocidicus	85.5765	1644	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_014655595.1	s__Streptomyces griseocarneus	85.4397	1625	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	85.2227	1595	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:56,082] [INFO] GTDB search result was written to GCF_017876625.1_ASM1787662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:56,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:56,085] [INFO] DFAST_QC result json was written to GCF_017876625.1_ASM1787662v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:56,085] [INFO] DFAST_QC completed!
[2024-01-24 13:20:56,085] [INFO] Total running time: 0h3m23s