[2024-01-24 14:12:45,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference
[2024-01-24 14:12:46,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:46,934] [INFO] Task started: Prodigal
[2024-01-24 14:12:46,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg580d7e3a-e40e-4239-9bb6-5740843bc358/GCF_000718985.1_ASM71898v1_genomic.fna.gz | prodigal -d GCF_000718985.1_ASM71898v1_genomic.fna/cds.fna -a GCF_000718985.1_ASM71898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:02,928] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:02,928] [INFO] Task started: HMMsearch
[2024-01-24 14:13:02,929] [INFO] Running command: hmmsearch --tblout GCF_000718985.1_ASM71898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/reference_markers.hmm GCF_000718985.1_ASM71898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:03,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:03,269] [INFO] Found 6/6 markers.
[2024-01-24 14:13:03,324] [INFO] Query marker FASTA was written to GCF_000718985.1_ASM71898v1_genomic.fna/markers.fasta
[2024-01-24 14:13:03,324] [INFO] Task started: Blastn
[2024-01-24 14:13:03,324] [INFO] Running command: blastn -query GCF_000718985.1_ASM71898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/reference_markers.fasta -out GCF_000718985.1_ASM71898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:04,673] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:04,677] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:04,677] [INFO] Target genome list was writen to GCF_000718985.1_ASM71898v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:04,687] [INFO] Task started: fastANI
[2024-01-24 14:13:04,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg580d7e3a-e40e-4239-9bb6-5740843bc358/GCF_000718985.1_ASM71898v1_genomic.fna.gz --refList GCF_000718985.1_ASM71898v1_genomic.fna/target_genomes.txt --output GCF_000718985.1_ASM71898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:30,584] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:30,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:30,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:30,610] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:30,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:30,611] [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 megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	100.0	1899	1902	95	conclusive
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	87.7051	1417	1902	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	87.3719	1406	1902	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	87.3401	1399	1902	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	87.3226	1385	1902	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	87.3192	1402	1902	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	87.2575	1390	1902	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	86.7825	1363	1902	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	80.9655	991	1902	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.9627	1049	1902	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.8991	907	1902	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.8842	1005	1902	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.8824	917	1902	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.8055	1061	1902	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	80.6426	1029	1902	95	below_threshold
Streptomyces otsuchiensis	strain=OTB305	GCA_004305975.1	2681388	2681388	type	True	80.3865	787	1902	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	80.0135	752	1902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:30,613] [INFO] DFAST Taxonomy check result was written to GCF_000718985.1_ASM71898v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:30,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:30,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:30,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/checkm_data
[2024-01-24 14:13:30,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:30,674] [INFO] Task started: CheckM
[2024-01-24 14:13:30,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718985.1_ASM71898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718985.1_ASM71898v1_genomic.fna/checkm_input GCF_000718985.1_ASM71898v1_genomic.fna/checkm_result
[2024-01-24 14:14:58,775] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:58,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:58,803] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:58,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:58,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718985.1_ASM71898v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:58,804] [INFO] Task started: Blastn
[2024-01-24 14:14:58,804] [INFO] Running command: blastn -query GCF_000718985.1_ASM71898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbefe06e8-6b98-42ce-b778-4bf27aa34738/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718985.1_ASM71898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:01,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:01,070] [INFO] Selected 13 target genomes.
[2024-01-24 14:15:01,070] [INFO] Target genome list was writen to GCF_000718985.1_ASM71898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:01,080] [INFO] Task started: fastANI
[2024-01-24 14:15:01,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg580d7e3a-e40e-4239-9bb6-5740843bc358/GCF_000718985.1_ASM71898v1_genomic.fna.gz --refList GCF_000718985.1_ASM71898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718985.1_ASM71898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:21,666] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:21,683] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:21,684] [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_000718985.1	s__Streptomyces megasporus	100.0	1899	1902	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_900110735.1	s__Streptomyces radiopugnans	87.6636	1421	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843305.1	s__Streptomyces barkulensis	87.3405	1398	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_009709575.1	s__Streptomyces taklimakanensis	87.3394	1410	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114215.1	s__Streptomyces pini	87.318	1402	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	N/A	N/A	N/A	N/A	1	-
GCF_017114865.1	s__Streptomyces verrucosisporus	87.2286	1392	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	86.7837	1362	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426325.1	s__Streptomyces sp000426325	81.3801	996	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.50	96.50	0.91	0.91	2	-
GCA_003519485.1	s__Streptomyces sp003519485	81.1809	698	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741875.1	s__Streptomyces coffeae	80.9333	981	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158915.1	s__Streptomyces himastatinicus	80.8973	1070	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.59	95.41	0.86	0.82	5	-
GCF_017676365.1	s__Streptomyces oryzae	80.8756	911	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	80.8316	984	1902	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 14:15:21,685] [INFO] GTDB search result was written to GCF_000718985.1_ASM71898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:21,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:21,690] [INFO] DFAST_QC result json was written to GCF_000718985.1_ASM71898v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:21,691] [INFO] DFAST_QC completed!
[2024-01-24 14:15:21,691] [INFO] Total running time: 0h2m36s