[2024-01-24 14:12:04,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:04,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:04,214] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference
[2024-01-24 14:12:05,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,467] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg0feba4e4-f5ee-47f8-9f2d-5e0c1d5f102a/GCF_002982015.1_ASM298201v1_genomic.fna.gz | prodigal -d GCF_002982015.1_ASM298201v1_genomic.fna/cds.fna -a GCF_002982015.1_ASM298201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:21,096] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:21,096] [INFO] Task started: HMMsearch
[2024-01-24 14:12:21,096] [INFO] Running command: hmmsearch --tblout GCF_002982015.1_ASM298201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/reference_markers.hmm GCF_002982015.1_ASM298201v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:21,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:21,429] [INFO] Found 6/6 markers.
[2024-01-24 14:12:21,483] [INFO] Query marker FASTA was written to GCF_002982015.1_ASM298201v1_genomic.fna/markers.fasta
[2024-01-24 14:12:21,483] [INFO] Task started: Blastn
[2024-01-24 14:12:21,484] [INFO] Running command: blastn -query GCF_002982015.1_ASM298201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/reference_markers.fasta -out GCF_002982015.1_ASM298201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:22,864] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:22,868] [INFO] Selected 24 target genomes.
[2024-01-24 14:12:22,868] [INFO] Target genome list was writen to GCF_002982015.1_ASM298201v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:22,882] [INFO] Task started: fastANI
[2024-01-24 14:12:22,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg0feba4e4-f5ee-47f8-9f2d-5e0c1d5f102a/GCF_002982015.1_ASM298201v1_genomic.fna.gz --refList GCF_002982015.1_ASM298201v1_genomic.fna/target_genomes.txt --output GCF_002982015.1_ASM298201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:03,949] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:03,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:03,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:03,982] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:03,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:03,983] [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 lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	89.4943	1335	1763	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	84.4781	1202	1763	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	83.8333	1086	1763	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	83.6588	755	1763	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.4836	1105	1763	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.4087	955	1763	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	83.3996	1091	1763	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	83.3817	950	1763	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	83.3669	1101	1763	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	83.1981	1150	1763	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	83.1929	1150	1763	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	83.0636	1113	1763	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.9624	1207	1763	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.8871	1159	1763	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	82.868	1126	1763	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.8454	1094	1763	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	82.6333	1113	1763	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	82.549	1052	1763	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.465	1060	1763	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	82.1488	1096	1763	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	82.126	1113	1763	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	81.9977	1041	1763	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	81.9822	1041	1763	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	81.8162	986	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,984] [INFO] DFAST Taxonomy check result was written to GCF_002982015.1_ASM298201v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:03,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:03,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:03,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/checkm_data
[2024-01-24 14:13:03,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:04,052] [INFO] Task started: CheckM
[2024-01-24 14:13:04,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002982015.1_ASM298201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002982015.1_ASM298201v1_genomic.fna/checkm_input GCF_002982015.1_ASM298201v1_genomic.fna/checkm_result
[2024-01-24 14:13:54,210] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:54,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:54,235] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:54,236] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:54,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002982015.1_ASM298201v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:54,237] [INFO] Task started: Blastn
[2024-01-24 14:13:54,237] [INFO] Running command: blastn -query GCF_002982015.1_ASM298201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0df878-46a6-4906-a984-165eede0016c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002982015.1_ASM298201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:56,436] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:56,444] [INFO] Selected 21 target genomes.
[2024-01-24 14:13:56,444] [INFO] Target genome list was writen to GCF_002982015.1_ASM298201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:56,489] [INFO] Task started: fastANI
[2024-01-24 14:13:56,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg0feba4e4-f5ee-47f8-9f2d-5e0c1d5f102a/GCF_002982015.1_ASM298201v1_genomic.fna.gz --refList GCF_002982015.1_ASM298201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002982015.1_ASM298201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:31,000] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:31,022] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:31,022] [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_002982015.1	s__Streptomyces sp002982015	100.0	1738	1763	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_004353505.1	s__Streptomyces sp004353505	84.7324	1199	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_009739905.1	s__Streptomyces ficellus	84.6196	1218	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649735.1	s__Streptomyces lavendofoliae	84.4537	1205	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646665.1	s__Streptomyces albulus_A	84.4461	1219	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	84.4048	1210	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_000716335.1	s__Streptomyces sp000716335	83.9786	1171	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280125.1	s__Streptomyces sp001280125	83.5359	1141	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_000478605.2	s__Streptomyces thermolilacinus	83.4867	1093	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648195.1	s__Streptomyces purpureus	83.4619	1108	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_001484625.1	s__Streptomyces kanasensis	83.3583	1101	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000258595.1	s__Streptomyces somaliensis_A	83.3488	920	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377145.1	s__Streptomyces sp000377145	83.3208	1114	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614205.1	s__Streptomyces sp018614205	83.2415	1039	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	83.2054	1147	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271805.1	s__Streptomyces sp008271805	83.2039	1075	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042045.1	s__Streptomyces sp008042045	82.9747	1142	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	82.957	1207	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489615.1	s__Streptomyces sp014489615	82.8875	1158	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280195.1	s__Streptomyces galbus	82.1123	1101	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCA_014651175.1	s__Streptomyces clavifer	82.0026	1040	1763	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:31,024] [INFO] GTDB search result was written to GCF_002982015.1_ASM298201v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:31,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:31,029] [INFO] DFAST_QC result json was written to GCF_002982015.1_ASM298201v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:31,029] [INFO] DFAST_QC completed!
[2024-01-24 14:14:31,029] [INFO] Total running time: 0h2m27s