[2024-01-24 11:21:07,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference
[2024-01-24 11:21:11,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,964] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b424923-110a-431c-b9f5-5c90f28dbd2f/GCF_014649495.1_ASM1464949v1_genomic.fna.gz | prodigal -d GCF_014649495.1_ASM1464949v1_genomic.fna/cds.fna -a GCF_014649495.1_ASM1464949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:37,428] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:37,429] [INFO] Task started: HMMsearch
[2024-01-24 11:21:37,429] [INFO] Running command: hmmsearch --tblout GCF_014649495.1_ASM1464949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/reference_markers.hmm GCF_014649495.1_ASM1464949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:37,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:37,785] [INFO] Found 6/6 markers.
[2024-01-24 11:21:37,855] [INFO] Query marker FASTA was written to GCF_014649495.1_ASM1464949v1_genomic.fna/markers.fasta
[2024-01-24 11:21:37,855] [INFO] Task started: Blastn
[2024-01-24 11:21:37,856] [INFO] Running command: blastn -query GCF_014649495.1_ASM1464949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/reference_markers.fasta -out GCF_014649495.1_ASM1464949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:39,195] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:39,198] [INFO] Selected 18 target genomes.
[2024-01-24 11:21:39,198] [INFO] Target genome list was writen to GCF_014649495.1_ASM1464949v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:39,205] [INFO] Task started: fastANI
[2024-01-24 11:21:39,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b424923-110a-431c-b9f5-5c90f28dbd2f/GCF_014649495.1_ASM1464949v1_genomic.fna.gz --refList GCF_014649495.1_ASM1464949v1_genomic.fna/target_genomes.txt --output GCF_014649495.1_ASM1464949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:21,364] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:21,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:21,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:21,379] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:22:21,380] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:22:21,380] [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 filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	100.0	3034	3037	95	inconclusive
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	96.7318	2691	3037	95	inconclusive
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	90.2353	2235	3037	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	90.1335	2194	3037	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	90.1128	2164	3037	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	88.5385	2117	3037	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	88.4279	2076	3037	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	88.1697	2094	3037	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	88.1503	2061	3037	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	88.0936	1984	3037	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	87.9211	2013	3037	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	87.9116	2094	3037	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	87.8824	1949	3037	95	below_threshold
Streptomyces griseochromogenes	strain=ATCC 14511	GCA_001542625.2	68214	68214	type	True	87.6243	2165	3037	95	below_threshold
Streptomyces griseochromogenes	strain=DSM 40499	GCA_017874495.1	68214	68214	type	True	87.5768	2169	3037	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.1812	1412	3037	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.007	1908	3037	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.4328	1423	3037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:21,381] [INFO] DFAST Taxonomy check result was written to GCF_014649495.1_ASM1464949v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:21,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:21,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:21,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/checkm_data
[2024-01-24 11:22:21,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:21,467] [INFO] Task started: CheckM
[2024-01-24 11:22:21,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649495.1_ASM1464949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649495.1_ASM1464949v1_genomic.fna/checkm_input GCF_014649495.1_ASM1464949v1_genomic.fna/checkm_result
[2024-01-24 11:24:37,032] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:37,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:37,061] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:37,061] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:37,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649495.1_ASM1464949v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:37,062] [INFO] Task started: Blastn
[2024-01-24 11:24:37,062] [INFO] Running command: blastn -query GCF_014649495.1_ASM1464949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8edd19-9353-43c3-a39c-8300361a1f36/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649495.1_ASM1464949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:39,250] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:39,254] [INFO] Selected 20 target genomes.
[2024-01-24 11:24:39,255] [INFO] Target genome list was writen to GCF_014649495.1_ASM1464949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:39,294] [INFO] Task started: fastANI
[2024-01-24 11:24:39,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b424923-110a-431c-b9f5-5c90f28dbd2f/GCF_014649495.1_ASM1464949v1_genomic.fna.gz --refList GCF_014649495.1_ASM1464949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649495.1_ASM1464949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:25:25,805] [INFO] Task succeeded: fastANI
[2024-01-24 11:25:25,824] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:25:25,825] [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_014649495.1	s__Streptomyces filipinensis	100.0	3034	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	conclusive
GCF_001735805.1	s__Streptomyces fodineus	90.2353	2235	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715785.1	s__Streptomyces puniciscabiei	90.1602	2190	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.70	95.42	0.91	0.82	3	-
GCF_009604455.1	s__Streptomyces sp009604455	90.0876	2158	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497445.1	s__Streptomyces roseochromogenus	89.8421	2143	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953885.1	s__Streptomyces sp001953885	89.7217	2186	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650595.1	s__Streptomyces alanosinicus	89.4024	2117	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	88.8985	2040	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796285.1	s__Streptomyces broussonetiae	88.5613	2113	3037	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	88.4182	2077	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_016741855.1	s__Streptomyces musisoli	88.159	2094	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	88.1321	2100	3037	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	88.1143	1991	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_000716535.1	s__Streptomyces flaveolus_A	88.0409	2029	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002155905.1	s__Streptomyces tricolor	88.0284	1630	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_001513965.1	s__Streptomyces cellostaticus	87.9297	2091	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650035.1	s__Streptomyces lucensis	87.8958	1890	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741775.1	s__Streptomyces actinomycinicus	87.8371	2057	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542625.1	s__Streptomyces griseochromogenes	87.6386	2163	3037	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016432725.1	s__Streptomyces sp016432725	86.9966	1888	3037	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 11:25:25,826] [INFO] GTDB search result was written to GCF_014649495.1_ASM1464949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:25:25,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:25:25,831] [INFO] DFAST_QC result json was written to GCF_014649495.1_ASM1464949v1_genomic.fna/dqc_result.json
[2024-01-24 11:25:25,831] [INFO] DFAST_QC completed!
[2024-01-24 11:25:25,831] [INFO] Total running time: 0h4m18s