[2024-01-25 17:58:35,719] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference
[2024-01-25 17:58:36,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,991] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg6675a9e9-1b63-49ec-95c4-6c3a94f25642/GCF_022271435.1_ASM2227143v1_genomic.fna.gz | prodigal -d GCF_022271435.1_ASM2227143v1_genomic.fna/cds.fna -a GCF_022271435.1_ASM2227143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:02,924] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:02,924] [INFO] Task started: HMMsearch
[2024-01-25 17:59:02,924] [INFO] Running command: hmmsearch --tblout GCF_022271435.1_ASM2227143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/reference_markers.hmm GCF_022271435.1_ASM2227143v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:03,267] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:03,269] [INFO] Found 6/6 markers.
[2024-01-25 17:59:03,332] [INFO] Query marker FASTA was written to GCF_022271435.1_ASM2227143v1_genomic.fna/markers.fasta
[2024-01-25 17:59:03,333] [INFO] Task started: Blastn
[2024-01-25 17:59:03,333] [INFO] Running command: blastn -query GCF_022271435.1_ASM2227143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/reference_markers.fasta -out GCF_022271435.1_ASM2227143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:04,629] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:04,635] [INFO] Selected 11 target genomes.
[2024-01-25 17:59:04,636] [INFO] Target genome list was writen to GCF_022271435.1_ASM2227143v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:04,646] [INFO] Task started: fastANI
[2024-01-25 17:59:04,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg6675a9e9-1b63-49ec-95c4-6c3a94f25642/GCF_022271435.1_ASM2227143v1_genomic.fna.gz --refList GCF_022271435.1_ASM2227143v1_genomic.fna/target_genomes.txt --output GCF_022271435.1_ASM2227143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:28,558] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:28,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:28,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:28,567] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:59:28,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:28,567] [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 monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	100.0	3034	3039	95	conclusive
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	99.9076	2826	3039	95	conclusive
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	94.3931	2588	3039	95	below_threshold
Streptomyces chrestomyceticus	strain=NBRC 13444	GCA_003865135.1	68185	68185	type	True	94.1769	2522	3039	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	89.9372	2303	3039	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	89.7325	2316	3039	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	89.7031	2349	3039	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	83.9056	1544	3039	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	80.675	1316	3039	95	below_threshold
Mycobacterium intracellulare subsp. yongonense	strain=05-1390	GCA_000418535.2	1203599	1767	type	True	75.8624	314	3039	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	74.7968	122	3039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:28,569] [INFO] DFAST Taxonomy check result was written to GCF_022271435.1_ASM2227143v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:28,569] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:28,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:28,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/checkm_data
[2024-01-25 17:59:28,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:28,655] [INFO] Task started: CheckM
[2024-01-25 17:59:28,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022271435.1_ASM2227143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022271435.1_ASM2227143v1_genomic.fna/checkm_input GCF_022271435.1_ASM2227143v1_genomic.fna/checkm_result
[2024-01-25 18:01:46,776] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:46,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:46,805] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:46,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:46,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022271435.1_ASM2227143v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:46,807] [INFO] Task started: Blastn
[2024-01-25 18:01:46,807] [INFO] Running command: blastn -query GCF_022271435.1_ASM2227143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4676dfdf-5ceb-4c68-ace5-65aff0edafdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_022271435.1_ASM2227143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:48,992] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:48,996] [INFO] Selected 10 target genomes.
[2024-01-25 18:01:48,996] [INFO] Target genome list was writen to GCF_022271435.1_ASM2227143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:49,003] [INFO] Task started: fastANI
[2024-01-25 18:01:49,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg6675a9e9-1b63-49ec-95c4-6c3a94f25642/GCF_022271435.1_ASM2227143v1_genomic.fna.gz --refList GCF_022271435.1_ASM2227143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022271435.1_ASM2227143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:09,659] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:09,667] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:09,667] [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_000715845.1	s__Streptomyces monomycini	99.8995	2827	3039	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_003865135.1	s__Streptomyces chrestomyceticus	94.1838	2521	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.95	95.89	0.90	0.88	4	-
GCF_001905005.1	s__Streptomyces sp001905005	91.605	2369	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008634025.1	s__Streptomyces albofaciens	89.9142	2306	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720725.1	s__Streptomyces rimosus_A	89.8071	2267	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704655.1	s__Streptomyces rimosus	89.7661	2337	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	96.53	0.95	0.89	49	-
GCF_014654675.1	s__Streptomyces spiralis	80.6002	1345	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_017312405.1	s__Mycobacterium sp017312405	75.9173	305	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_016704655.1	s__RPQJ01 sp016704655	74.9072	86	3039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	74.7991	121	3039	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:09,668] [INFO] GTDB search result was written to GCF_022271435.1_ASM2227143v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:09,669] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:09,673] [INFO] DFAST_QC result json was written to GCF_022271435.1_ASM2227143v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:09,673] [INFO] DFAST_QC completed!
[2024-01-25 18:02:09,673] [INFO] Total running time: 0h3m34s