[2024-01-24 11:12:58,187] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,189] [INFO] DQC Reference Directory: /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference
[2024-01-24 11:12:59,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,706] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,706] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb55e8f4-79c4-4374-9156-cc8cb8d20e49/GCF_003073355.1_ASM307335v1_genomic.fna.gz | prodigal -d GCF_003073355.1_ASM307335v1_genomic.fna/cds.fna -a GCF_003073355.1_ASM307335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:20,368] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:20,368] [INFO] Task started: HMMsearch
[2024-01-24 11:13:20,368] [INFO] Running command: hmmsearch --tblout GCF_003073355.1_ASM307335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/reference_markers.hmm GCF_003073355.1_ASM307335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:20,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:20,777] [INFO] Found 6/6 markers.
[2024-01-24 11:13:20,835] [INFO] Query marker FASTA was written to GCF_003073355.1_ASM307335v1_genomic.fna/markers.fasta
[2024-01-24 11:13:20,836] [INFO] Task started: Blastn
[2024-01-24 11:13:20,836] [INFO] Running command: blastn -query GCF_003073355.1_ASM307335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/reference_markers.fasta -out GCF_003073355.1_ASM307335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:22,081] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:22,084] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:22,084] [INFO] Target genome list was writen to GCF_003073355.1_ASM307335v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:22,088] [INFO] Task started: fastANI
[2024-01-24 11:13:22,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb55e8f4-79c4-4374-9156-cc8cb8d20e49/GCF_003073355.1_ASM307335v1_genomic.fna.gz --refList GCF_003073355.1_ASM307335v1_genomic.fna/target_genomes.txt --output GCF_003073355.1_ASM307335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:45,251] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:45,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:45,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:45,265] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:45,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:45,266] [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 scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	100.0	2439	2458	95	conclusive
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	99.9803	2433	2458	95	conclusive
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	86.6385	1386	2458	95	below_threshold
Streptomyces odonnellii	strain=NRRL B-24891	GCA_000981895.1	1417980	1417980	type	True	86.5393	1453	2458	95	below_threshold
Streptomyces corynorhini	strain=AC230	GCA_003346515.1	2282652	2282652	type	True	85.804	1429	2458	95	below_threshold
Streptomyces paludis	strain=GSSD-12	GCA_003344965.1	2282738	2282738	type	True	85.7345	1516	2458	95	below_threshold
Streptomyces liangshanensis	strain=QMT-12	GCA_011694815.1	2717324	2717324	type	True	84.7766	1456	2458	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.0405	1338	2458	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.9814	1202	2458	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.6884	957	2458	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.6213	971	2458	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.8638	1268	2458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:45,268] [INFO] DFAST Taxonomy check result was written to GCF_003073355.1_ASM307335v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:45,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:45,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:45,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/checkm_data
[2024-01-24 11:13:45,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:45,354] [INFO] Task started: CheckM
[2024-01-24 11:13:45,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003073355.1_ASM307335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003073355.1_ASM307335v1_genomic.fna/checkm_input GCF_003073355.1_ASM307335v1_genomic.fna/checkm_result
[2024-01-24 11:14:52,457] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:52,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:52,477] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:52,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:52,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003073355.1_ASM307335v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:52,478] [INFO] Task started: Blastn
[2024-01-24 11:14:52,478] [INFO] Running command: blastn -query GCF_003073355.1_ASM307335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2b22c42-72f1-4ad2-a4ae-7ca9a0b22d63/dqc_reference/reference_markers_gtdb.fasta -out GCF_003073355.1_ASM307335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:54,421] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:54,426] [INFO] Selected 8 target genomes.
[2024-01-24 11:14:54,426] [INFO] Target genome list was writen to GCF_003073355.1_ASM307335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:54,434] [INFO] Task started: fastANI
[2024-01-24 11:14:54,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb55e8f4-79c4-4374-9156-cc8cb8d20e49/GCF_003073355.1_ASM307335v1_genomic.fna.gz --refList GCF_003073355.1_ASM307335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003073355.1_ASM307335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:11,801] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:11,812] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:11,812] [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_000718095.1	s__Streptomyces scopuliridis	99.9803	2433	2458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_004151105.1	s__Streptomyces sp004151105	93.4608	1943	2458	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	86.6467	1385	2458	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	86.5002	1457	2458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.86	95.86	0.85	0.85	2	-
GCF_003346515.1	s__Streptomyces corynorhini	85.7692	1434	2458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344965.1	s__Streptomyces paludis	85.6998	1521	2458	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	84.7538	1461	2458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002009175.1	s__Streptomyces niveus_A	83.9471	1470	2458	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 11:15:11,816] [INFO] GTDB search result was written to GCF_003073355.1_ASM307335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:11,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:11,820] [INFO] DFAST_QC result json was written to GCF_003073355.1_ASM307335v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:11,820] [INFO] DFAST_QC completed!
[2024-01-24 11:15:11,820] [INFO] Total running time: 0h2m14s