[2024-01-24 11:12:55,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:55,770] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:55,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference
[2024-01-24 11:12:57,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:57,058] [INFO] Task started: Prodigal
[2024-01-24 11:12:57,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg222f9f9e-346c-4a32-bef9-305736177d63/GCF_014650735.1_ASM1465073v1_genomic.fna.gz | prodigal -d GCF_014650735.1_ASM1465073v1_genomic.fna/cds.fna -a GCF_014650735.1_ASM1465073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:28,406] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:28,406] [INFO] Task started: HMMsearch
[2024-01-24 11:13:28,406] [INFO] Running command: hmmsearch --tblout GCF_014650735.1_ASM1465073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/reference_markers.hmm GCF_014650735.1_ASM1465073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:28,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:28,908] [INFO] Found 6/6 markers.
[2024-01-24 11:13:28,991] [INFO] Query marker FASTA was written to GCF_014650735.1_ASM1465073v1_genomic.fna/markers.fasta
[2024-01-24 11:13:28,991] [INFO] Task started: Blastn
[2024-01-24 11:13:28,991] [INFO] Running command: blastn -query GCF_014650735.1_ASM1465073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/reference_markers.fasta -out GCF_014650735.1_ASM1465073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:30,421] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:30,424] [INFO] Selected 18 target genomes.
[2024-01-24 11:13:30,425] [INFO] Target genome list was writen to GCF_014650735.1_ASM1465073v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:30,431] [INFO] Task started: fastANI
[2024-01-24 11:13:30,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg222f9f9e-346c-4a32-bef9-305736177d63/GCF_014650735.1_ASM1465073v1_genomic.fna.gz --refList GCF_014650735.1_ASM1465073v1_genomic.fna/target_genomes.txt --output GCF_014650735.1_ASM1465073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:10,534] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:10,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:10,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:10,549] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:14:10,549] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:14:10,549] [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 canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	100.0	3429	3437	95	inconclusive
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	97.2778	2859	3437	95	inconclusive
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	96.4382	2834	3437	95	inconclusive
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	93.8508	2442	3437	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.7285	2085	3437	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	89.6978	2123	3437	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.3268	1951	3437	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.2867	1964	3437	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.0952	1979	3437	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.4014	1450	3437	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.9424	1801	3437	95	below_threshold
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	84.6749	1788	3437	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.5884	1525	3437	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	80.4412	1388	3437	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	80.4123	1374	3437	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	76.401	857	3437	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	76.0905	230	3437	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	75.8004	236	3437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:10,551] [INFO] DFAST Taxonomy check result was written to GCF_014650735.1_ASM1465073v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:10,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:10,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:10,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/checkm_data
[2024-01-24 11:14:10,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:10,646] [INFO] Task started: CheckM
[2024-01-24 11:14:10,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650735.1_ASM1465073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650735.1_ASM1465073v1_genomic.fna/checkm_input GCF_014650735.1_ASM1465073v1_genomic.fna/checkm_result
[2024-01-24 11:16:49,219] [INFO] Task succeeded: CheckM
[2024-01-24 11:16:49,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:16:49,245] [INFO] ===== Completeness check finished =====
[2024-01-24 11:16:49,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:16:49,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650735.1_ASM1465073v1_genomic.fna/markers.fasta)
[2024-01-24 11:16:49,247] [INFO] Task started: Blastn
[2024-01-24 11:16:49,247] [INFO] Running command: blastn -query GCF_014650735.1_ASM1465073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg860fbbac-03b1-4275-974b-ad6a7b3e76b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650735.1_ASM1465073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:16:51,389] [INFO] Task succeeded: Blastn
[2024-01-24 11:16:51,393] [INFO] Selected 14 target genomes.
[2024-01-24 11:16:51,393] [INFO] Target genome list was writen to GCF_014650735.1_ASM1465073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:16:51,404] [INFO] Task started: fastANI
[2024-01-24 11:16:51,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg222f9f9e-346c-4a32-bef9-305736177d63/GCF_014650735.1_ASM1465073v1_genomic.fna.gz --refList GCF_014650735.1_ASM1465073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650735.1_ASM1465073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:17:24,434] [INFO] Task succeeded: fastANI
[2024-01-24 11:17:24,448] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:17:24,448] [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_014650115.1	s__Streptomyces olivaceoviridis	97.256	2862	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	conclusive
GCF_002920615.1	s__Streptomyces sp002920615	94.6588	2505	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_013046785.1	s__Streptomyces sp013046785	94.3309	2238	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	93.8649	2575	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_017526105.1	s__Streptomyces cyanogenus	90.7422	2103	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	90.6152	2217	3437	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	90.539	1787	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_016860525.1	s__Streptomyces rubradiris	89.2406	2000	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_016741775.1	s__Streptomyces actinomycinicus	89.1719	2023	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	83.2558	1678	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_900105415.1	s__Streptomyces sp900105415	81.605	1526	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014207445.1	s__Streptomyces candidus	80.8908	1283	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007595705.1	s__Streptomyces sp007595705	80.8567	1380	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718635.1	s__Streptomyces varsoviensis	80.3666	1408	3437	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:17:24,450] [INFO] GTDB search result was written to GCF_014650735.1_ASM1465073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:17:24,450] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:17:24,454] [INFO] DFAST_QC result json was written to GCF_014650735.1_ASM1465073v1_genomic.fna/dqc_result.json
[2024-01-24 11:17:24,455] [INFO] DFAST_QC completed!
[2024-01-24 11:17:24,455] [INFO] Total running time: 0h4m29s