[2024-01-24 14:14:31,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference
[2024-01-24 14:14:32,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,943] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg68cbb27a-22e1-4c37-aeb7-20140a7a46d5/GCF_014203645.1_ASM1420364v1_genomic.fna.gz | prodigal -d GCF_014203645.1_ASM1420364v1_genomic.fna/cds.fna -a GCF_014203645.1_ASM1420364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:15,067] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:15,068] [INFO] Task started: HMMsearch
[2024-01-24 14:15:15,068] [INFO] Running command: hmmsearch --tblout GCF_014203645.1_ASM1420364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/reference_markers.hmm GCF_014203645.1_ASM1420364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:15,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:15,504] [INFO] Found 6/6 markers.
[2024-01-24 14:15:15,577] [INFO] Query marker FASTA was written to GCF_014203645.1_ASM1420364v1_genomic.fna/markers.fasta
[2024-01-24 14:15:15,577] [INFO] Task started: Blastn
[2024-01-24 14:15:15,577] [INFO] Running command: blastn -query GCF_014203645.1_ASM1420364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/reference_markers.fasta -out GCF_014203645.1_ASM1420364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:16,916] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:16,921] [INFO] Selected 31 target genomes.
[2024-01-24 14:15:16,921] [INFO] Target genome list was writen to GCF_014203645.1_ASM1420364v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:16,943] [INFO] Task started: fastANI
[2024-01-24 14:15:16,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg68cbb27a-22e1-4c37-aeb7-20140a7a46d5/GCF_014203645.1_ASM1420364v1_genomic.fna.gz --refList GCF_014203645.1_ASM1420364v1_genomic.fna/target_genomes.txt --output GCF_014203645.1_ASM1420364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:11,952] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:11,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:11,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:11,976] [INFO] Found 31 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:11,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:11,977] [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 zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	100.0	2876	2880	95	conclusive
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	84.7458	1985	2880	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	80.7547	1018	2880	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	80.52	998	2880	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	80.3294	1268	2880	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	80.3257	1281	2880	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	80.3106	1288	2880	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.2526	1333	2880	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	80.2361	1302	2880	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	80.2264	1116	2880	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	80.2025	1055	2880	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	80.1972	1115	2880	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	80.1823	1115	2880	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	80.119	1165	2880	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.0629	1229	2880	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	80.0572	1221	2880	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	79.9638	1211	2880	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	79.9016	1019	2880	95	below_threshold
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	79.8924	989	2880	95	below_threshold
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	79.8806	968	2880	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.7248	1029	2880	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	79.6638	894	2880	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	79.5802	1160	2880	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	79.5801	1047	2880	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	79.5335	1173	2880	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	79.516	1096	2880	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	79.4901	1167	2880	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	79.3891	914	2880	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	79.3153	819	2880	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.2964	1022	2880	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	79.2588	960	2880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:11,980] [INFO] DFAST Taxonomy check result was written to GCF_014203645.1_ASM1420364v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:11,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:11,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:11,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/checkm_data
[2024-01-24 14:16:11,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:12,081] [INFO] Task started: CheckM
[2024-01-24 14:16:12,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203645.1_ASM1420364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203645.1_ASM1420364v1_genomic.fna/checkm_input GCF_014203645.1_ASM1420364v1_genomic.fna/checkm_result
[2024-01-24 14:18:09,227] [INFO] Task succeeded: CheckM
[2024-01-24 14:18:09,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.54%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:18:09,254] [INFO] ===== Completeness check finished =====
[2024-01-24 14:18:09,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:18:09,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203645.1_ASM1420364v1_genomic.fna/markers.fasta)
[2024-01-24 14:18:09,256] [INFO] Task started: Blastn
[2024-01-24 14:18:09,256] [INFO] Running command: blastn -query GCF_014203645.1_ASM1420364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76bed254-47ef-4809-a9ec-567d48dee2a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203645.1_ASM1420364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:18:11,329] [INFO] Task succeeded: Blastn
[2024-01-24 14:18:11,333] [INFO] Selected 21 target genomes.
[2024-01-24 14:18:11,334] [INFO] Target genome list was writen to GCF_014203645.1_ASM1420364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:18:11,377] [INFO] Task started: fastANI
[2024-01-24 14:18:11,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg68cbb27a-22e1-4c37-aeb7-20140a7a46d5/GCF_014203645.1_ASM1420364v1_genomic.fna.gz --refList GCF_014203645.1_ASM1420364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203645.1_ASM1420364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:18:50,219] [INFO] Task succeeded: fastANI
[2024-01-24 14:18:50,241] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:18:50,242] [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_014203645.1	s__Streptomyces zagrosensis	100.0	2876	2880	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_014295035.1	s__Streptomyces buecherae	84.7207	1990	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
GCA_018114805.1	s__Streptomyces philanthi	84.3228	1739	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	80.7576	1016	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	80.4784	1029	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968685.2	s__Streptomyces antioxidans	80.3421	1199	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405925.1	s__Streptomyces antimycoticus	80.2232	1306	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCF_003389455.1	s__Streptomyces inhibens	80.2094	1054	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002891295.1	s__Streptomyces eurocidicus	80.2077	1121	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	3	-
GCF_016031615.1	s__Streptomyces pactum	80.1833	1292	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003519485.1	s__Streptomyces sp003519485	80.1092	664	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935125.1	s__Streptomyces natalensis	80.0632	1076	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	80.0577	1215	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_017916255.1	s__Streptomyces mobaraensis	79.9793	1058	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_003121295.1	s__Streptomyces orinoci	79.8544	975	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	79.6702	1065	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	79.6078	1052	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	79.3167	1056	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	79.2127	1119	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	79.1653	1013	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847285.1	s__Streptomyces sp002847285	78.7295	945	2880	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:18:50,244] [INFO] GTDB search result was written to GCF_014203645.1_ASM1420364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:18:50,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:18:50,250] [INFO] DFAST_QC result json was written to GCF_014203645.1_ASM1420364v1_genomic.fna/dqc_result.json
[2024-01-24 14:18:50,250] [INFO] DFAST_QC completed!
[2024-01-24 14:18:50,251] [INFO] Total running time: 0h4m19s