[2024-01-24 12:36:35,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,454] [INFO] DQC Reference Directory: /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference
[2024-01-24 12:36:36,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,666] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgb56932d9-8d88-47b0-865f-e1297dc09d18/GCF_016741855.1_ASM1674185v1_genomic.fna.gz | prodigal -d GCF_016741855.1_ASM1674185v1_genomic.fna/cds.fna -a GCF_016741855.1_ASM1674185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:03,073] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:03,073] [INFO] Task started: HMMsearch
[2024-01-24 12:37:03,073] [INFO] Running command: hmmsearch --tblout GCF_016741855.1_ASM1674185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/reference_markers.hmm GCF_016741855.1_ASM1674185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:03,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:03,545] [INFO] Found 6/6 markers.
[2024-01-24 12:37:03,618] [INFO] Query marker FASTA was written to GCF_016741855.1_ASM1674185v1_genomic.fna/markers.fasta
[2024-01-24 12:37:03,619] [INFO] Task started: Blastn
[2024-01-24 12:37:03,619] [INFO] Running command: blastn -query GCF_016741855.1_ASM1674185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/reference_markers.fasta -out GCF_016741855.1_ASM1674185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:04,971] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:04,975] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:04,976] [INFO] Target genome list was writen to GCF_016741855.1_ASM1674185v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:05,008] [INFO] Task started: fastANI
[2024-01-24 12:37:05,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgb56932d9-8d88-47b0-865f-e1297dc09d18/GCF_016741855.1_ASM1674185v1_genomic.fna.gz --refList GCF_016741855.1_ASM1674185v1_genomic.fna/target_genomes.txt --output GCF_016741855.1_ASM1674185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:47,826] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:47,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:47,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:47,843] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:47,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:47,844] [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 musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	100.0	3060	3065	95	conclusive
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	92.7867	2464	3065	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	92.7714	2408	3065	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	89.8501	2093	3065	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	89.8377	2104	3065	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	89.8144	2093	3065	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	89.4855	2048	3065	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.2539	1923	3065	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.0986	1948	3065	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	89.0507	2025	3065	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	88.2279	2087	3065	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.0655	2014	3065	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	87.4786	1984	3065	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	87.1986	1949	3065	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	87.1204	2071	3065	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.1242	1400	3065	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.024	1626	3065	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.9557	1871	3065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:47,845] [INFO] DFAST Taxonomy check result was written to GCF_016741855.1_ASM1674185v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:47,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:47,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:47,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/checkm_data
[2024-01-24 12:37:47,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:47,934] [INFO] Task started: CheckM
[2024-01-24 12:37:47,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016741855.1_ASM1674185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016741855.1_ASM1674185v1_genomic.fna/checkm_input GCF_016741855.1_ASM1674185v1_genomic.fna/checkm_result
[2024-01-24 12:40:01,074] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:01,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:01,109] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:01,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:01,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016741855.1_ASM1674185v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:01,111] [INFO] Task started: Blastn
[2024-01-24 12:40:01,111] [INFO] Running command: blastn -query GCF_016741855.1_ASM1674185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb96a828f-dd46-4776-aae5-8c76655b2e7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016741855.1_ASM1674185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:03,351] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:03,354] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:03,354] [INFO] Target genome list was writen to GCF_016741855.1_ASM1674185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:03,367] [INFO] Task started: fastANI
[2024-01-24 12:40:03,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgb56932d9-8d88-47b0-865f-e1297dc09d18/GCF_016741855.1_ASM1674185v1_genomic.fna.gz --refList GCF_016741855.1_ASM1674185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016741855.1_ASM1674185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:48,029] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:48,050] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:48,051] [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_016741855.1	s__Streptomyces musisoli	100.0	3060	3065	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_014203595.1	s__Streptomyces echinatus	92.7889	2464	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009865385.1	s__Streptomyces sp009865385	90.5731	1864	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.9845	2125	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.9466	2140	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046785.1	s__Streptomyces sp013046785	89.8909	2007	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.8581	2092	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_002920615.1	s__Streptomyces sp002920615	89.8317	2081	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	89.788	2158	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	89.7803	1720	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_016741775.1	s__Streptomyces actinomycinicus	89.5463	2135	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649295.1	s__Streptomyces libani_A	89.3666	2025	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720835.1	s__Streptomyces achromogenes	89.2598	1922	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	89.0686	2021	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_009796285.1	s__Streptomyces broussonetiae	87.4455	1988	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827595.1	s__Streptomyces sp007827595	87.2336	2107	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	87.2084	1948	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCA_016432725.1	s__Streptomyces sp016432725	86.8068	1959	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896895.1	s__Streptomyces misionensis_A	86.7759	1741	3065	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 12:40:48,052] [INFO] GTDB search result was written to GCF_016741855.1_ASM1674185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:48,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:48,058] [INFO] DFAST_QC result json was written to GCF_016741855.1_ASM1674185v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:48,058] [INFO] DFAST_QC completed!
[2024-01-24 12:40:48,058] [INFO] Total running time: 0h4m13s