[2024-01-24 11:59:05,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference
[2024-01-24 11:59:06,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,259] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg69209d41-bd36-4880-bf8f-f29cc84d6e87/GCF_014656195.1_ASM1465619v1_genomic.fna.gz | prodigal -d GCF_014656195.1_ASM1465619v1_genomic.fna/cds.fna -a GCF_014656195.1_ASM1465619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:31,740] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:31,740] [INFO] Task started: HMMsearch
[2024-01-24 11:59:31,741] [INFO] Running command: hmmsearch --tblout GCF_014656195.1_ASM1465619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/reference_markers.hmm GCF_014656195.1_ASM1465619v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:32,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:32,101] [INFO] Found 6/6 markers.
[2024-01-24 11:59:32,178] [INFO] Query marker FASTA was written to GCF_014656195.1_ASM1465619v1_genomic.fna/markers.fasta
[2024-01-24 11:59:32,178] [INFO] Task started: Blastn
[2024-01-24 11:59:32,178] [INFO] Running command: blastn -query GCF_014656195.1_ASM1465619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/reference_markers.fasta -out GCF_014656195.1_ASM1465619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:33,574] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:33,578] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:33,579] [INFO] Target genome list was writen to GCF_014656195.1_ASM1465619v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:33,584] [INFO] Task started: fastANI
[2024-01-24 11:59:33,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg69209d41-bd36-4880-bf8f-f29cc84d6e87/GCF_014656195.1_ASM1465619v1_genomic.fna.gz --refList GCF_014656195.1_ASM1465619v1_genomic.fna/target_genomes.txt --output GCF_014656195.1_ASM1465619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:04,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:04,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:04,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:04,368] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:04,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:04,368] [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	89.0329	2071	3055	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	88.873	1760	3055	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	88.6274	1968	3055	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	85.8425	1995	3055	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	84.075	1793	3055	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	83.8789	1570	3055	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	83.6566	1665	3055	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	82.7342	1617	3055	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	82.6109	1649	3055	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.3793	1435	3055	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	79.2509	1029	3055	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	78.2979	1218	3055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:04,370] [INFO] DFAST Taxonomy check result was written to GCF_014656195.1_ASM1465619v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:04,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:04,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:04,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/checkm_data
[2024-01-24 12:00:04,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:04,459] [INFO] Task started: CheckM
[2024-01-24 12:00:04,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656195.1_ASM1465619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656195.1_ASM1465619v1_genomic.fna/checkm_input GCF_014656195.1_ASM1465619v1_genomic.fna/checkm_result
[2024-01-24 12:02:01,182] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:01,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:01,216] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:01,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:01,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656195.1_ASM1465619v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:01,217] [INFO] Task started: Blastn
[2024-01-24 12:02:01,217] [INFO] Running command: blastn -query GCF_014656195.1_ASM1465619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dab17df-3718-496f-aba6-b87bd78e6be6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656195.1_ASM1465619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:03,459] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:03,467] [INFO] Selected 14 target genomes.
[2024-01-24 12:02:03,467] [INFO] Target genome list was writen to GCF_014656195.1_ASM1465619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:03,478] [INFO] Task started: fastANI
[2024-01-24 12:02:03,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg69209d41-bd36-4880-bf8f-f29cc84d6e87/GCF_014656195.1_ASM1465619v1_genomic.fna.gz --refList GCF_014656195.1_ASM1465619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656195.1_ASM1465619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:42,650] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:42,665] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:42,665] [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_014656195.1	s__Kitasatospora xanthocidica	100.0	3051	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000716875.1	s__Kitasatospora novaecaesareae	91.803	1952	3055	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	91.152	2175	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.37	99.37	0.96	0.96	2	-
GCF_000719705.1	s__Kitasatospora sp000719705	90.6489	2068	3055	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	90.223	2218	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.73	98.73	0.93	0.93	2	-
GCF_015776785.2	s__Kitasatospora sp015776785	90.1153	1757	3055	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	89.6194	1840	3055	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	89.117	2100	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596465.1	s__Kitasatospora sp014596465	89.0114	1962	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001188955.3	s__Kitasatospora aureofaciens	89.0011	2075	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.54	97.86	0.95	0.85	10	-
GCF_000961885.1	s__Kitasatospora rubellomurina	88.6554	1964	3055	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	88.1757	1970	3055	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	87.7578	1885	3055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	87.6527	1974	3055	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 12:02:42,667] [INFO] GTDB search result was written to GCF_014656195.1_ASM1465619v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:42,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:42,671] [INFO] DFAST_QC result json was written to GCF_014656195.1_ASM1465619v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:42,671] [INFO] DFAST_QC completed!
[2024-01-24 12:02:42,671] [INFO] Total running time: 0h3m38s