[2024-01-24 13:47:11,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference
[2024-01-24 13:47:13,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,133] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg30d25811-e270-4374-b2b8-4d625e0cf383/GCF_000719175.1_ASM71917v1_genomic.fna.gz | prodigal -d GCF_000719175.1_ASM71917v1_genomic.fna/cds.fna -a GCF_000719175.1_ASM71917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:39,201] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:39,201] [INFO] Task started: HMMsearch
[2024-01-24 13:47:39,201] [INFO] Running command: hmmsearch --tblout GCF_000719175.1_ASM71917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/reference_markers.hmm GCF_000719175.1_ASM71917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:39,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:39,573] [INFO] Found 6/6 markers.
[2024-01-24 13:47:39,642] [INFO] Query marker FASTA was written to GCF_000719175.1_ASM71917v1_genomic.fna/markers.fasta
[2024-01-24 13:47:39,643] [INFO] Task started: Blastn
[2024-01-24 13:47:39,643] [INFO] Running command: blastn -query GCF_000719175.1_ASM71917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/reference_markers.fasta -out GCF_000719175.1_ASM71917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:41,086] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:41,091] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:41,091] [INFO] Target genome list was writen to GCF_000719175.1_ASM71917v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:41,103] [INFO] Task started: fastANI
[2024-01-24 13:47:41,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d25811-e270-4374-b2b8-4d625e0cf383/GCF_000719175.1_ASM71917v1_genomic.fna.gz --refList GCF_000719175.1_ASM71917v1_genomic.fna/target_genomes.txt --output GCF_000719175.1_ASM71917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:10,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:10,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:10,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:10,206] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:48:10,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:10,206] [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
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	99.968	2913	2967	95	conclusive
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	99.7392	2428	2967	95	conclusive
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	88.6907	1906	2967	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	85.466	1829	2967	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	83.7708	1465	2967	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	83.388	1653	2967	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	82.8786	1475	2967	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	82.8022	1474	2967	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	82.7273	1529	2967	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.6757	1443	2967	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	78.9365	1165	2967	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	78.3328	1063	2967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:10,207] [INFO] DFAST Taxonomy check result was written to GCF_000719175.1_ASM71917v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:10,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:10,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:10,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/checkm_data
[2024-01-24 13:48:10,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:10,291] [INFO] Task started: CheckM
[2024-01-24 13:48:10,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000719175.1_ASM71917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000719175.1_ASM71917v1_genomic.fna/checkm_input GCF_000719175.1_ASM71917v1_genomic.fna/checkm_result
[2024-01-24 13:49:36,604] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:36,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:36,629] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:36,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:36,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000719175.1_ASM71917v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:36,631] [INFO] Task started: Blastn
[2024-01-24 13:49:36,631] [INFO] Running command: blastn -query GCF_000719175.1_ASM71917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg854500a5-a4e1-48a0-b69a-5e3910f6c8fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000719175.1_ASM71917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:38,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:38,972] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:38,972] [INFO] Target genome list was writen to GCF_000719175.1_ASM71917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:38,981] [INFO] Task started: fastANI
[2024-01-24 13:49:38,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d25811-e270-4374-b2b8-4d625e0cf383/GCF_000719175.1_ASM71917v1_genomic.fna.gz --refList GCF_000719175.1_ASM71917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000719175.1_ASM71917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:11,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,527] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:11,528] [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_001188955.3	s__Kitasatospora aureofaciens	99.968	2913	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.54	97.86	0.95	0.85	10	conclusive
GCF_014596465.1	s__Kitasatospora sp014596465	91.0857	2028	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015776785.2	s__Kitasatospora sp015776785	90.73	1689	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716875.1	s__Kitasatospora novaecaesareae	89.7708	1795	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.97	99.97	0.97	0.97	2	-
GCF_900199205.1	s__Kitasatospora sp900199205	89.2728	2026	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.37	99.37	0.96	0.96	2	-
GCF_014656195.1	s__Kitasatospora xanthocidica	89.1095	2082	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905545.1	s__Kitasatospora sp001905545	88.8361	2038	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.73	98.73	0.93	0.93	2	-
GCF_000961885.1	s__Kitasatospora rubellomurina	88.6775	1907	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625365.1	s__Kitasatospora sp001625365	88.6051	1967	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596515.1	s__Kitasatospora sp014596515	88.334	1692	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192735.1	s__Kitasatospora aureofaciens_A	88.0292	1973	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009569385.1	s__Kitasatospora kaniharaensis	87.9082	1857	2967	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,529] [INFO] GTDB search result was written to GCF_000719175.1_ASM71917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:11,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:11,534] [INFO] DFAST_QC result json was written to GCF_000719175.1_ASM71917v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:11,534] [INFO] DFAST_QC completed!
[2024-01-24 13:50:11,535] [INFO] Total running time: 0h2m60s