[2024-01-24 12:16:08,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,292] [INFO] DQC Reference Directory: /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference
[2024-01-24 12:16:09,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,632] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg12d9c222-9d60-4263-80d3-3491afa95614/GCF_014649035.1_ASM1464903v1_genomic.fna.gz | prodigal -d GCF_014649035.1_ASM1464903v1_genomic.fna/cds.fna -a GCF_014649035.1_ASM1464903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:29,901] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:29,901] [INFO] Task started: HMMsearch
[2024-01-24 12:16:29,901] [INFO] Running command: hmmsearch --tblout GCF_014649035.1_ASM1464903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/reference_markers.hmm GCF_014649035.1_ASM1464903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:30,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:30,264] [INFO] Found 6/6 markers.
[2024-01-24 12:16:30,326] [INFO] Query marker FASTA was written to GCF_014649035.1_ASM1464903v1_genomic.fna/markers.fasta
[2024-01-24 12:16:30,327] [INFO] Task started: Blastn
[2024-01-24 12:16:30,327] [INFO] Running command: blastn -query GCF_014649035.1_ASM1464903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/reference_markers.fasta -out GCF_014649035.1_ASM1464903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,620] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,624] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:31,624] [INFO] Target genome list was writen to GCF_014649035.1_ASM1464903v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:31,626] [INFO] Task started: fastANI
[2024-01-24 12:16:31,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d9c222-9d60-4263-80d3-3491afa95614/GCF_014649035.1_ASM1464903v1_genomic.fna.gz --refList GCF_014649035.1_ASM1464903v1_genomic.fna/target_genomes.txt --output GCF_014649035.1_ASM1464903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:55,120] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:55,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:55,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:55,135] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:16:55,135] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:16:55,135] [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 sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	100.0	2470	2478	95	inconclusive
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	95.8884	2085	2478	95	inconclusive
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	95.0739	2125	2478	95	inconclusive
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	94.9474	1918	2478	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	91.8701	2053	2478	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	91.392	2045	2478	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	90.4748	1950	2478	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	89.0045	1539	2478	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.611	1589	2478	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.6268	1352	2478	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.5355	1434	2478	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.1023	1083	2478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:55,138] [INFO] DFAST Taxonomy check result was written to GCF_014649035.1_ASM1464903v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:55,138] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:55,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:55,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/checkm_data
[2024-01-24 12:16:55,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:55,220] [INFO] Task started: CheckM
[2024-01-24 12:16:55,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649035.1_ASM1464903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649035.1_ASM1464903v1_genomic.fna/checkm_input GCF_014649035.1_ASM1464903v1_genomic.fna/checkm_result
[2024-01-24 12:18:27,535] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:27,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:27,567] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:27,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:27,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649035.1_ASM1464903v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:27,569] [INFO] Task started: Blastn
[2024-01-24 12:18:27,569] [INFO] Running command: blastn -query GCF_014649035.1_ASM1464903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg039e2654-0693-46e3-8dc1-3aa79108786e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649035.1_ASM1464903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:29,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:29,562] [INFO] Selected 8 target genomes.
[2024-01-24 12:18:29,562] [INFO] Target genome list was writen to GCF_014649035.1_ASM1464903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:29,565] [INFO] Task started: fastANI
[2024-01-24 12:18:29,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d9c222-9d60-4263-80d3-3491afa95614/GCF_014649035.1_ASM1464903v1_genomic.fna.gz --refList GCF_014649035.1_ASM1464903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649035.1_ASM1464903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:45,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:45,623] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:45,623] [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_014649035.1	s__Streptomyces sindenensis	100.0	2470	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0775	95.83	95.78	0.85	0.84	5	conclusive
GCF_014648875.1	s__Streptomyces parvus	95.0775	2124	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2347	97.39	96.11	0.86	0.79	24	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	94.5734	2039	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_003501885.1	s__Streptomyces globisporus_D	94.4359	1856	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_001687325.1	s__Streptomyces sp001687325	94.4332	2057	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649555.1	s__Streptomyces globisporus	94.2838	2066	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.88	97.57	0.92	0.86	14	-
GCF_000718455.1	s__Streptomyces globisporus_A	94.1596	1970	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2621	N/A	N/A	N/A	N/A	1	-
GCF_018866325.1	s__Streptomyces sp001895105	93.2973	2006	2478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:45,625] [INFO] GTDB search result was written to GCF_014649035.1_ASM1464903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:45,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:45,630] [INFO] DFAST_QC result json was written to GCF_014649035.1_ASM1464903v1_genomic.fna/dqc_result.json
[2024-01-24 12:18:45,630] [INFO] DFAST_QC completed!
[2024-01-24 12:18:45,630] [INFO] Total running time: 0h2m37s