[2024-01-24 11:43:25,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference
[2024-01-24 11:43:30,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,061] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,061] [INFO] Running command: gunzip -c /var/lib/cwl/stga0844d36-c5a2-467f-97f9-ca5914f7293f/GCF_016741775.1_ASM1674177v1_genomic.fna.gz | prodigal -d GCF_016741775.1_ASM1674177v1_genomic.fna/cds.fna -a GCF_016741775.1_ASM1674177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:55,303] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:55,303] [INFO] Task started: HMMsearch
[2024-01-24 11:43:55,303] [INFO] Running command: hmmsearch --tblout GCF_016741775.1_ASM1674177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/reference_markers.hmm GCF_016741775.1_ASM1674177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:55,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:55,670] [INFO] Found 6/6 markers.
[2024-01-24 11:43:55,739] [INFO] Query marker FASTA was written to GCF_016741775.1_ASM1674177v1_genomic.fna/markers.fasta
[2024-01-24 11:43:55,740] [INFO] Task started: Blastn
[2024-01-24 11:43:55,740] [INFO] Running command: blastn -query GCF_016741775.1_ASM1674177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/reference_markers.fasta -out GCF_016741775.1_ASM1674177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:57,098] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:57,101] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:57,101] [INFO] Target genome list was writen to GCF_016741775.1_ASM1674177v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:57,126] [INFO] Task started: fastANI
[2024-01-24 11:43:57,127] [INFO] Running command: fastANI --query /var/lib/cwl/stga0844d36-c5a2-467f-97f9-ca5914f7293f/GCF_016741775.1_ASM1674177v1_genomic.fna.gz --refList GCF_016741775.1_ASM1674177v1_genomic.fna/target_genomes.txt --output GCF_016741775.1_ASM1674177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:39,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:39,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:39,877] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:39,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:39,878] [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	89.6232	2120	2893	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	89.387	2189	2893	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.3667	2149	2893	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	89.2861	2022	2893	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	89.263	2025	2893	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	89.2116	2029	2893	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	88.9664	1990	2893	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	88.4672	1846	2893	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	88.3842	1892	2893	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	88.3827	1894	2893	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	88.3364	1862	2893	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	88.3207	1922	2893	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	87.9414	1994	2893	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	87.8687	2004	2893	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	87.7168	1982	2893	95	below_threshold
Streptomyces malaysiense	strain=MUSC 136	GCA_000980885.2	1428626	1428626	type	True	86.3047	1726	2893	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.1259	1349	2893	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.8363	1821	2893	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.4581	1420	2893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,880] [INFO] DFAST Taxonomy check result was written to GCF_016741775.1_ASM1674177v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:39,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:39,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:39,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/checkm_data
[2024-01-24 11:44:39,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:39,959] [INFO] Task started: CheckM
[2024-01-24 11:44:39,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016741775.1_ASM1674177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016741775.1_ASM1674177v1_genomic.fna/checkm_input GCF_016741775.1_ASM1674177v1_genomic.fna/checkm_result
[2024-01-24 11:46:46,279] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:46,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:46,305] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:46,305] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:46,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016741775.1_ASM1674177v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:46,306] [INFO] Task started: Blastn
[2024-01-24 11:46:46,306] [INFO] Running command: blastn -query GCF_016741775.1_ASM1674177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56e88935-3034-4e05-b317-ef049ec9d1a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016741775.1_ASM1674177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:48,423] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:48,427] [INFO] Selected 20 target genomes.
[2024-01-24 11:46:48,428] [INFO] Target genome list was writen to GCF_016741775.1_ASM1674177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:48,444] [INFO] Task started: fastANI
[2024-01-24 11:46:48,445] [INFO] Running command: fastANI --query /var/lib/cwl/stga0844d36-c5a2-467f-97f9-ca5914f7293f/GCF_016741775.1_ASM1674177v1_genomic.fna.gz --refList GCF_016741775.1_ASM1674177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016741775.1_ASM1674177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:32,940] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:32,961] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:32,961] [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_016741775.1	s__Streptomyces actinomycinicus	100.0	2888	2893	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_016741855.1	s__Streptomyces musisoli	89.5904	2125	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	89.5099	2057	2893	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	89.3748	2191	2893	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	89.3646	1634	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_000716535.1	s__Streptomyces flaveolus_A	89.3377	2056	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	89.3362	2048	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920615.1	s__Streptomyces sp002920615	89.3268	2014	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	89.3177	2018	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_013046785.1	s__Streptomyces sp013046785	89.2125	1951	2893	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	88.8136	1974	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718775.1	s__Streptomyces sp000718775	88.7796	1841	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675325.1	s__Streptomyces sp003675325	88.7129	1930	2893	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	88.3503	1860	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	N/A	N/A	N/A	N/A	1	-
GCF_016860525.1	s__Streptomyces rubradiris	88.3472	1899	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_014649115.1	s__Streptomyces eurythermus	88.2933	1926	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_001735805.1	s__Streptomyces fodineus	87.883	2001	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604455.1	s__Streptomyces sp009604455	87.8658	1977	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242805.1	s__Streptomyces diastatochromogenes	87.6859	2005	2893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.15	97.09	0.86	0.86	5	-
GCF_001636945.1	s__Streptomyces sp001636945	87.6784	1876	2893	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 11:47:32,963] [INFO] GTDB search result was written to GCF_016741775.1_ASM1674177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:32,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:32,968] [INFO] DFAST_QC result json was written to GCF_016741775.1_ASM1674177v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:32,968] [INFO] DFAST_QC completed!
[2024-01-24 11:47:32,968] [INFO] Total running time: 0h4m8s