[2024-01-25 19:12:05,520] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:05,521] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:05,521] [INFO] DQC Reference Directory: /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference
[2024-01-25 19:12:06,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:06,614] [INFO] Task started: Prodigal
[2024-01-25 19:12:06,614] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb1d63a2-5d41-4d62-b7be-a5bdf554005f/GCF_015912875.1_ASM1591287v1_genomic.fna.gz | prodigal -d GCF_015912875.1_ASM1591287v1_genomic.fna/cds.fna -a GCF_015912875.1_ASM1591287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:24,288] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:24,288] [INFO] Task started: HMMsearch
[2024-01-25 19:12:24,288] [INFO] Running command: hmmsearch --tblout GCF_015912875.1_ASM1591287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/reference_markers.hmm GCF_015912875.1_ASM1591287v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:24,616] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:24,617] [INFO] Found 6/6 markers.
[2024-01-25 19:12:24,682] [INFO] Query marker FASTA was written to GCF_015912875.1_ASM1591287v1_genomic.fna/markers.fasta
[2024-01-25 19:12:24,682] [INFO] Task started: Blastn
[2024-01-25 19:12:24,682] [INFO] Running command: blastn -query GCF_015912875.1_ASM1591287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/reference_markers.fasta -out GCF_015912875.1_ASM1591287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:25,866] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:25,868] [INFO] Selected 11 target genomes.
[2024-01-25 19:12:25,869] [INFO] Target genome list was writen to GCF_015912875.1_ASM1591287v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:25,875] [INFO] Task started: fastANI
[2024-01-25 19:12:25,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1d63a2-5d41-4d62-b7be-a5bdf554005f/GCF_015912875.1_ASM1591287v1_genomic.fna.gz --refList GCF_015912875.1_ASM1591287v1_genomic.fna/target_genomes.txt --output GCF_015912875.1_ASM1591287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:45,206] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:45,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:45,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:45,215] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 19:12:45,215] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:45,215] [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 clavuligerus	strain=ATCC 27064	GCA_000148465.1	1901	1901	type	True	99.9659	2137	2139	95	conclusive
Streptomyces clavuligerus	strain=ATCC 27064	GCA_005519465.1	1901	1901	type	True	99.8482	2013	2139	95	conclusive
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000163875.1	1901	1901	suspected-type	True	99.8191	2013	2139	95	conclusive
Streptomyces clavuligerus	strain=NCIMB 14335	GCA_015912435.1	1901	1901	type	True	99.8189	1896	2139	95	conclusive
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	99.812	1833	2139	95	conclusive
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000154925.1	1901	1901	suspected-type	True	99.2597	1695	2139	95	conclusive
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.8235	995	2139	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.7357	1056	2139	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.4095	825	2139	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.2608	835	2139	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	79.9361	950	2139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:45,217] [INFO] DFAST Taxonomy check result was written to GCF_015912875.1_ASM1591287v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:45,219] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:45,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:45,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/checkm_data
[2024-01-25 19:12:45,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:45,303] [INFO] Task started: CheckM
[2024-01-25 19:12:45,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015912875.1_ASM1591287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015912875.1_ASM1591287v1_genomic.fna/checkm_input GCF_015912875.1_ASM1591287v1_genomic.fna/checkm_result
[2024-01-25 19:13:45,982] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:45,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:46,005] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:46,005] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:46,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015912875.1_ASM1591287v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:46,008] [INFO] Task started: Blastn
[2024-01-25 19:13:46,008] [INFO] Running command: blastn -query GCF_015912875.1_ASM1591287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb88da38b-bf1e-4b47-ba8b-6a59a75ef290/dqc_reference/reference_markers_gtdb.fasta -out GCF_015912875.1_ASM1591287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:47,890] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:47,893] [INFO] Selected 21 target genomes.
[2024-01-25 19:13:47,893] [INFO] Target genome list was writen to GCF_015912875.1_ASM1591287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:47,922] [INFO] Task started: fastANI
[2024-01-25 19:13:47,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1d63a2-5d41-4d62-b7be-a5bdf554005f/GCF_015912875.1_ASM1591287v1_genomic.fna.gz --refList GCF_015912875.1_ASM1591287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015912875.1_ASM1591287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:23,860] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:23,873] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:23,874] [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_005519465.1	s__Streptomyces clavuligerus	99.8607	2012	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.68	0.97	0.92	18	conclusive
GCF_009600885.1	s__Streptomyces jumonjinensis_A	84.5056	1271	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.98	97.98	0.89	0.89	2	-
GCF_014651115.1	s__Streptomyces inusitatus	84.2271	1219	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715635.1	s__Streptomyces sp006715635	82.2974	985	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	82.0896	1021	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_000377145.1	s__Streptomyces sp000377145	82.0896	1017	2139	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	81.9283	1022	2139	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	81.8974	974	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005517195.1	s__Streptomyces exfoliatus_B	81.8556	1018	2139	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	81.8416	1098	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	81.8035	929	2139	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	81.734	1056	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	81.5324	1051	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_000478605.2	s__Streptomyces thermolilacinus	81.5192	941	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	81.4591	1009	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014654895.1	s__Streptomyces filamentosus	81.4386	1063	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_900105415.1	s__Streptomyces sp900105415	81.4356	1047	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_008271805.1	s__Streptomyces sp008271805	81.4099	945	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649755.1	s__Streptomyces litmocidini	81.4044	1015	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_014656075.1	s__Streptomyces hydrogenans	81.3973	1062	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCF_014650175.1	s__Streptomyces termitum	81.3174	1044	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:23,875] [INFO] GTDB search result was written to GCF_015912875.1_ASM1591287v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:23,876] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:23,879] [INFO] DFAST_QC result json was written to GCF_015912875.1_ASM1591287v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:23,879] [INFO] DFAST_QC completed!
[2024-01-25 19:14:23,880] [INFO] Total running time: 0h2m18s