[2024-01-24 13:37:26,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:26,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:26,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference
[2024-01-24 13:37:28,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:28,114] [INFO] Task started: Prodigal
[2024-01-24 13:37:28,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6298ff7-86b5-4ce9-b406-f64f443a8c74/GCF_020819595.1_ASM2081959v1_genomic.fna.gz | prodigal -d GCF_020819595.1_ASM2081959v1_genomic.fna/cds.fna -a GCF_020819595.1_ASM2081959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:54,305] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:54,305] [INFO] Task started: HMMsearch
[2024-01-24 13:37:54,305] [INFO] Running command: hmmsearch --tblout GCF_020819595.1_ASM2081959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/reference_markers.hmm GCF_020819595.1_ASM2081959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:54,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:54,661] [INFO] Found 6/6 markers.
[2024-01-24 13:37:54,735] [INFO] Query marker FASTA was written to GCF_020819595.1_ASM2081959v1_genomic.fna/markers.fasta
[2024-01-24 13:37:54,736] [INFO] Task started: Blastn
[2024-01-24 13:37:54,736] [INFO] Running command: blastn -query GCF_020819595.1_ASM2081959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/reference_markers.fasta -out GCF_020819595.1_ASM2081959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:56,100] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:56,105] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:56,106] [INFO] Target genome list was writen to GCF_020819595.1_ASM2081959v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:56,199] [INFO] Task started: fastANI
[2024-01-24 13:37:56,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6298ff7-86b5-4ce9-b406-f64f443a8c74/GCF_020819595.1_ASM2081959v1_genomic.fna.gz --refList GCF_020819595.1_ASM2081959v1_genomic.fna/target_genomes.txt --output GCF_020819595.1_ASM2081959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:35,736] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:35,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:35,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:35,751] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:35,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:35,752] [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 barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	100.0	2959	2964	95	conclusive
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	92.5644	2266	2964	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	91.2653	2287	2964	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	90.2009	2134	2964	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	90.1251	2162	2964	95	below_threshold
Streptomyces yokosukanensis	strain=DSM 40224	GCA_001514035.1	67386	67386	type	True	89.8982	2142	2964	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	89.5475	2115	2964	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	88.2486	1965	2964	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	88.1366	1995	2964	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	88.1047	1978	2964	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	87.9424	1948	2964	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	87.4436	1827	2964	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	87.4331	1800	2964	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	87.4251	1804	2964	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.6729	1411	2964	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.4255	1917	2964	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.6534	1409	2964	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:35,754] [INFO] DFAST Taxonomy check result was written to GCF_020819595.1_ASM2081959v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:35,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:35,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:35,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/checkm_data
[2024-01-24 13:38:35,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:35,839] [INFO] Task started: CheckM
[2024-01-24 13:38:35,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020819595.1_ASM2081959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020819595.1_ASM2081959v1_genomic.fna/checkm_input GCF_020819595.1_ASM2081959v1_genomic.fna/checkm_result
[2024-01-24 13:40:39,963] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:39,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:40:40,004] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:40,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:40,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020819595.1_ASM2081959v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:40,006] [INFO] Task started: Blastn
[2024-01-24 13:40:40,006] [INFO] Running command: blastn -query GCF_020819595.1_ASM2081959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a91c80-c95f-4b80-a8fb-14a121234067/dqc_reference/reference_markers_gtdb.fasta -out GCF_020819595.1_ASM2081959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,168] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:42,168] [INFO] Target genome list was writen to GCF_020819595.1_ASM2081959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:42,852] [INFO] Task started: fastANI
[2024-01-24 13:40:42,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6298ff7-86b5-4ce9-b406-f64f443a8c74/GCF_020819595.1_ASM2081959v1_genomic.fna.gz --refList GCF_020819595.1_ASM2081959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020819595.1_ASM2081959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:27,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:27,328] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:41:27,329] [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_006715785.1	s__Streptomyces puniciscabiei	92.5384	2270	2964	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	92.3834	2274	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735805.1	s__Streptomyces fodineus	91.2531	2289	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649495.1	s__Streptomyces filipinensis	90.1782	2138	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_000497445.1	s__Streptomyces roseochromogenus	90.1769	2181	2964	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	90.1491	2240	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514035.1	s__Streptomyces yokosukanensis	89.8983	2142	2964	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	89.5815	2110	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	89.5098	2072	2964	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	88.9672	2146	2964	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	88.3916	1979	2964	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	88.2487	1959	2964	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	88.2485	1965	2964	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	88.2194	2010	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_013046785.1	s__Streptomyces sp013046785	88.2001	1894	2964	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	88.0008	1978	2964	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	87.7278	1666	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	87.4422	1829	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_016860525.1	s__Streptomyces rubradiris	87.4375	1799	2964	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,331] [INFO] GTDB search result was written to GCF_020819595.1_ASM2081959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:27,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:27,336] [INFO] DFAST_QC result json was written to GCF_020819595.1_ASM2081959v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:27,336] [INFO] DFAST_QC completed!
[2024-01-24 13:41:27,336] [INFO] Total running time: 0h4m0s