[2024-01-24 13:21:57,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:57,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:57,154] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference
[2024-01-24 13:21:58,440] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:58,441] [INFO] Task started: Prodigal
[2024-01-24 13:21:58,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ac7315c-68ef-414f-8e17-665e42908e7e/GCF_016755875.1_ASM1675587v1_genomic.fna.gz | prodigal -d GCF_016755875.1_ASM1675587v1_genomic.fna/cds.fna -a GCF_016755875.1_ASM1675587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:28,128] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:28,129] [INFO] Task started: HMMsearch
[2024-01-24 13:22:28,129] [INFO] Running command: hmmsearch --tblout GCF_016755875.1_ASM1675587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/reference_markers.hmm GCF_016755875.1_ASM1675587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:28,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:28,578] [INFO] Found 6/6 markers.
[2024-01-24 13:22:28,663] [INFO] Query marker FASTA was written to GCF_016755875.1_ASM1675587v1_genomic.fna/markers.fasta
[2024-01-24 13:22:28,664] [INFO] Task started: Blastn
[2024-01-24 13:22:28,664] [INFO] Running command: blastn -query GCF_016755875.1_ASM1675587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/reference_markers.fasta -out GCF_016755875.1_ASM1675587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,070] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:30,070] [INFO] Target genome list was writen to GCF_016755875.1_ASM1675587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:30,074] [INFO] Task started: fastANI
[2024-01-24 13:22:30,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac7315c-68ef-414f-8e17-665e42908e7e/GCF_016755875.1_ASM1675587v1_genomic.fna.gz --refList GCF_016755875.1_ASM1675587v1_genomic.fna/target_genomes.txt --output GCF_016755875.1_ASM1675587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:59,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:59,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:59,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:59,711] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:59,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:59,711] [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 spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	100.0	2938	2948	95	conclusive
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	93.4387	2311	2948	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	93.4337	2340	2948	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	93.4035	2346	2948	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	91.9627	2165	2948	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	91.9113	2173	2948	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	89.6001	2074	2948	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	88.1217	1964	2948	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.9841	1370	2948	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.2682	1246	2948	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.1229	1150	2948	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	80.8693	1359	2948	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.5882	1225	2948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,713] [INFO] DFAST Taxonomy check result was written to GCF_016755875.1_ASM1675587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:59,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:59,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:59,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/checkm_data
[2024-01-24 13:22:59,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:59,796] [INFO] Task started: CheckM
[2024-01-24 13:22:59,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016755875.1_ASM1675587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016755875.1_ASM1675587v1_genomic.fna/checkm_input GCF_016755875.1_ASM1675587v1_genomic.fna/checkm_result
[2024-01-24 13:25:20,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:20,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:20,069] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:20,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:20,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016755875.1_ASM1675587v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:20,070] [INFO] Task started: Blastn
[2024-01-24 13:25:20,070] [INFO] Running command: blastn -query GCF_016755875.1_ASM1675587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc11051f-fa56-4194-83aa-aafc14a6df77/dqc_reference/reference_markers_gtdb.fasta -out GCF_016755875.1_ASM1675587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:22,287] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:22,291] [INFO] Selected 8 target genomes.
[2024-01-24 13:25:22,292] [INFO] Target genome list was writen to GCF_016755875.1_ASM1675587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:22,317] [INFO] Task started: fastANI
[2024-01-24 13:25:22,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac7315c-68ef-414f-8e17-665e42908e7e/GCF_016755875.1_ASM1675587v1_genomic.fna.gz --refList GCF_016755875.1_ASM1675587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016755875.1_ASM1675587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:44,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:44,069] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:44,070] [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_016755875.1	s__Streptomyces spororaveus	100.0	2939	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017639205.1	s__Streptomyces nojiriensis	93.3812	2349	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008642275.1	s__Streptomyces venezuelae_E	93.1255	2194	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716685.1	s__Streptomyces virginiae_A	93.0199	2313	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.46	95.91	0.89	0.84	3	-
GCF_003148825.1	s__Streptomyces sp003148825	92.8464	2225	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.84	95.84	0.87	0.86	3	-
GCF_002080455.1	s__Streptomyces sp002080455	92.1246	2159	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.34	98.21	0.92	0.90	7	-
GCF_014650695.1	s__Streptomyces avidinii	91.9208	2173	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648795.1	s__Streptomyces cinnamonensis	89.5598	2085	2948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.18	96.61	0.93	0.87	24	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:44,072] [INFO] GTDB search result was written to GCF_016755875.1_ASM1675587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:44,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:44,076] [INFO] DFAST_QC result json was written to GCF_016755875.1_ASM1675587v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:44,076] [INFO] DFAST_QC completed!
[2024-01-24 13:25:44,076] [INFO] Total running time: 0h3m47s