[2024-01-24 11:26:27,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference
[2024-01-24 11:26:29,046] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,048] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg0692af54-9962-4bfd-9c19-7f83f829ce01/GCF_014650755.1_ASM1465075v1_genomic.fna.gz | prodigal -d GCF_014650755.1_ASM1465075v1_genomic.fna/cds.fna -a GCF_014650755.1_ASM1465075v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:49,043] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:49,044] [INFO] Task started: HMMsearch
[2024-01-24 11:26:49,044] [INFO] Running command: hmmsearch --tblout GCF_014650755.1_ASM1465075v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/reference_markers.hmm GCF_014650755.1_ASM1465075v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:49,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:49,448] [INFO] Found 6/6 markers.
[2024-01-24 11:26:49,515] [INFO] Query marker FASTA was written to GCF_014650755.1_ASM1465075v1_genomic.fna/markers.fasta
[2024-01-24 11:26:49,515] [INFO] Task started: Blastn
[2024-01-24 11:26:49,515] [INFO] Running command: blastn -query GCF_014650755.1_ASM1465075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/reference_markers.fasta -out GCF_014650755.1_ASM1465075v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:50,828] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:50,831] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:50,831] [INFO] Target genome list was writen to GCF_014650755.1_ASM1465075v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:50,837] [INFO] Task started: fastANI
[2024-01-24 11:26:50,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg0692af54-9962-4bfd-9c19-7f83f829ce01/GCF_014650755.1_ASM1465075v1_genomic.fna.gz --refList GCF_014650755.1_ASM1465075v1_genomic.fna/target_genomes.txt --output GCF_014650755.1_ASM1465075v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:18,004] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:18,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:18,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:18,016] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:27:18,016] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:27:18,017] [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 chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	100.0	2338	2340	95	inconclusive
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	99.6251	1688	2340	95	inconclusive
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	95.4308	1635	2340	95	inconclusive
Streptomyces flavidovirens	strain=DSM 40150	GCA_000429085.1	67298	67298	type	True	90.5195	1761	2340	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.1397	1439	2340	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	83.0725	1326	2340	95	below_threshold
Streptomyces candidus	strain=DSM 40141	GCA_014207445.1	67283	67283	type	True	82.9453	1365	2340	95	below_threshold
Streptomyces candidus	strain=JCM 4629	GCA_014655855.1	67283	67283	type	True	82.9186	1363	2340	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	82.8054	1325	2340	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.278	1464	2340	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.024	1273	2340	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	81.6418	1190	2340	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	81.4656	1350	2340	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.4619	1263	2340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:18,018] [INFO] DFAST Taxonomy check result was written to GCF_014650755.1_ASM1465075v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:18,019] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:18,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:18,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/checkm_data
[2024-01-24 11:27:18,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:18,087] [INFO] Task started: CheckM
[2024-01-24 11:27:18,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650755.1_ASM1465075v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650755.1_ASM1465075v1_genomic.fna/checkm_input GCF_014650755.1_ASM1465075v1_genomic.fna/checkm_result
[2024-01-24 11:28:44,390] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:44,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:44,417] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:44,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:44,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650755.1_ASM1465075v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:44,418] [INFO] Task started: Blastn
[2024-01-24 11:28:44,418] [INFO] Running command: blastn -query GCF_014650755.1_ASM1465075v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769b69e6-318f-49b1-9479-07aa49183da6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650755.1_ASM1465075v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:46,366] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:46,370] [INFO] Selected 8 target genomes.
[2024-01-24 11:28:46,371] [INFO] Target genome list was writen to GCF_014650755.1_ASM1465075v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:46,378] [INFO] Task started: fastANI
[2024-01-24 11:28:46,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg0692af54-9962-4bfd-9c19-7f83f829ce01/GCF_014650755.1_ASM1465075v1_genomic.fna.gz --refList GCF_014650755.1_ASM1465075v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650755.1_ASM1465075v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:02,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:02,285] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:02,286] [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_014650755.1	s__Streptomyces chryseus	100.0	2338	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	99.26	99.24	0.89	0.85	3	conclusive
GCF_005981925.1	s__Streptomyces albidochromogenes	95.4437	1634	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCF_001746415.1	s__Streptomyces agglomeratus	90.7262	1900	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_000429085.1	s__Streptomyces flavidovirens	90.5342	1759	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.82	0.82	2	-
GCF_018614035.1	s__Streptomyces sp018614035	89.7588	1759	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614615.1	s__Streptomyces sp018614615	89.6546	1777	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003719395.1	s__Streptomyces altiplanensis	89.1821	1582	2340	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
GCF_015160855.1	s__Streptomyces ferrugineus	81.6846	1398	2340	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 11:29:02,287] [INFO] GTDB search result was written to GCF_014650755.1_ASM1465075v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:02,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:02,309] [INFO] DFAST_QC result json was written to GCF_014650755.1_ASM1465075v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:02,310] [INFO] DFAST_QC completed!
[2024-01-24 11:29:02,310] [INFO] Total running time: 0h2m35s