[2024-01-24 12:14:10,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference
[2024-01-24 12:14:11,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,680] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgd86e7584-f13c-4ddb-b0af-95eaa6820ad1/GCF_003346515.1_ASM334651v1_genomic.fna.gz | prodigal -d GCF_003346515.1_ASM334651v1_genomic.fna/cds.fna -a GCF_003346515.1_ASM334651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:30,880] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:30,881] [INFO] Task started: HMMsearch
[2024-01-24 12:14:30,881] [INFO] Running command: hmmsearch --tblout GCF_003346515.1_ASM334651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/reference_markers.hmm GCF_003346515.1_ASM334651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:31,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:31,316] [INFO] Found 6/6 markers.
[2024-01-24 12:14:31,374] [INFO] Query marker FASTA was written to GCF_003346515.1_ASM334651v1_genomic.fna/markers.fasta
[2024-01-24 12:14:31,375] [INFO] Task started: Blastn
[2024-01-24 12:14:31,375] [INFO] Running command: blastn -query GCF_003346515.1_ASM334651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/reference_markers.fasta -out GCF_003346515.1_ASM334651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:32,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:32,689] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:32,690] [INFO] Target genome list was writen to GCF_003346515.1_ASM334651v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:32,701] [INFO] Task started: fastANI
[2024-01-24 12:14:32,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgd86e7584-f13c-4ddb-b0af-95eaa6820ad1/GCF_003346515.1_ASM334651v1_genomic.fna.gz --refList GCF_003346515.1_ASM334651v1_genomic.fna/target_genomes.txt --output GCF_003346515.1_ASM334651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:58,720] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:58,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:58,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:58,733] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:58,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:58,734] [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 corynorhini	strain=AC230	GCA_003346515.1	2282652	2282652	type	True	100.0	2326	2344	95	conclusive
Streptomyces paludis	strain=GSSD-12	GCA_003344965.1	2282738	2282738	type	True	87.4445	1677	2344	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	85.8407	1419	2344	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	85.7572	1522	2344	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	84.7642	1239	2344	95	below_threshold
Streptomyces odonnellii	strain=NRRL B-24891	GCA_000981895.1	1417980	1417980	type	True	84.6201	1282	2344	95	below_threshold
Streptomyces liangshanensis	strain=QMT-12	GCA_011694815.1	2717324	2717324	type	True	83.9264	1372	2344	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.5468	1240	2344	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	82.5446	1106	2344	95	below_threshold
Streptomyces gelaticus	strain=JCM 4376	GCA_014649535.1	285446	285446	type	True	82.4788	1219	2344	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	82.3665	1182	2344	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	82.1163	1233	2344	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.7916	1186	2344	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.7495	1294	2344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:58,748] [INFO] DFAST Taxonomy check result was written to GCF_003346515.1_ASM334651v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:58,749] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:58,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:58,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/checkm_data
[2024-01-24 12:14:58,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:58,820] [INFO] Task started: CheckM
[2024-01-24 12:14:58,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003346515.1_ASM334651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003346515.1_ASM334651v1_genomic.fna/checkm_input GCF_003346515.1_ASM334651v1_genomic.fna/checkm_result
[2024-01-24 12:16:32,004] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:32,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:32,034] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:32,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:32,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003346515.1_ASM334651v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:32,035] [INFO] Task started: Blastn
[2024-01-24 12:16:32,035] [INFO] Running command: blastn -query GCF_003346515.1_ASM334651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4634d19f-1836-47e0-af5b-03decc6b0dac/dqc_reference/reference_markers_gtdb.fasta -out GCF_003346515.1_ASM334651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:34,018] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:34,022] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:34,022] [INFO] Target genome list was writen to GCF_003346515.1_ASM334651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:34,049] [INFO] Task started: fastANI
[2024-01-24 12:16:34,049] [INFO] Running command: fastANI --query /var/lib/cwl/stgd86e7584-f13c-4ddb-b0af-95eaa6820ad1/GCF_003346515.1_ASM334651v1_genomic.fna.gz --refList GCF_003346515.1_ASM334651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003346515.1_ASM334651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:56,191] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:56,204] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:56,205] [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_003346515.1	s__Streptomyces corynorhini	100.0	2326	2344	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_003344965.1	s__Streptomyces paludis	87.4294	1678	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718095.1	s__Streptomyces scopuliridis	85.7813	1519	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_004151105.1	s__Streptomyces sp004151105	85.4443	1554	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700515.1	s__Streptomyces lushanensis	84.7688	1239	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981895.1	s__Streptomyces odonnellii	84.6378	1279	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.86	95.86	0.85	0.85	2	-
GCF_000719775.1	s__Streptomyces sp000719775	84.0268	1486	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694815.1	s__Streptomyces liangshanensis	83.9415	1370	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010384365.1	s__Streptomyces sp010384365	83.1996	1327	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_004795035.1	s__Streptomyces sp004795035	82.464	1195	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003846175.1	s__Streptomyces sp003846175	82.2742	1326	2344	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:56,206] [INFO] GTDB search result was written to GCF_003346515.1_ASM334651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:56,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:56,212] [INFO] DFAST_QC result json was written to GCF_003346515.1_ASM334651v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:56,212] [INFO] DFAST_QC completed!
[2024-01-24 12:16:56,212] [INFO] Total running time: 0h2m46s