[2024-01-24 13:46:30,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:30,139] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:30,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference
[2024-01-24 13:46:31,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:31,400] [INFO] Task started: Prodigal
[2024-01-24 13:46:31,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f630dc2-a3f0-4722-abba-d8fb06faceb4/GCF_007828955.1_ASM782895v1_genomic.fna.gz | prodigal -d GCF_007828955.1_ASM782895v1_genomic.fna/cds.fna -a GCF_007828955.1_ASM782895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:53,373] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:53,373] [INFO] Task started: HMMsearch
[2024-01-24 13:46:53,374] [INFO] Running command: hmmsearch --tblout GCF_007828955.1_ASM782895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/reference_markers.hmm GCF_007828955.1_ASM782895v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:53,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:53,742] [INFO] Found 6/6 markers.
[2024-01-24 13:46:53,814] [INFO] Query marker FASTA was written to GCF_007828955.1_ASM782895v1_genomic.fna/markers.fasta
[2024-01-24 13:46:53,815] [INFO] Task started: Blastn
[2024-01-24 13:46:53,815] [INFO] Running command: blastn -query GCF_007828955.1_ASM782895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/reference_markers.fasta -out GCF_007828955.1_ASM782895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:55,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:55,216] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:55,217] [INFO] Target genome list was writen to GCF_007828955.1_ASM782895v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:55,234] [INFO] Task started: fastANI
[2024-01-24 13:46:55,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f630dc2-a3f0-4722-abba-d8fb06faceb4/GCF_007828955.1_ASM782895v1_genomic.fna.gz --refList GCF_007828955.1_ASM782895v1_genomic.fna/target_genomes.txt --output GCF_007828955.1_ASM782895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:25,600] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:25,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:25,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:25,612] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:25,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:25,613] [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 atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	100.0	2620	2623	95	conclusive
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	85.2977	1634	2623	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	84.7172	1593	2623	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	84.6426	1619	2623	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	84.6239	1618	2623	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	84.0189	1262	2623	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.8585	1419	2623	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	83.8261	1488	2623	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.8082	1423	2623	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	83.6104	1515	2623	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	83.2958	1363	2623	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.6052	1273	2623	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.4922	776	2623	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.0803	1029	2623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,615] [INFO] DFAST Taxonomy check result was written to GCF_007828955.1_ASM782895v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:25,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:25,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:25,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/checkm_data
[2024-01-24 13:47:25,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:25,688] [INFO] Task started: CheckM
[2024-01-24 13:47:25,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007828955.1_ASM782895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007828955.1_ASM782895v1_genomic.fna/checkm_input GCF_007828955.1_ASM782895v1_genomic.fna/checkm_result
[2024-01-24 13:48:49,199] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:49,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.80%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:48:49,225] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:49,225] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:49,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007828955.1_ASM782895v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:49,226] [INFO] Task started: Blastn
[2024-01-24 13:48:49,226] [INFO] Running command: blastn -query GCF_007828955.1_ASM782895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf665389b-35b4-4570-9aca-37505a673596/dqc_reference/reference_markers_gtdb.fasta -out GCF_007828955.1_ASM782895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:51,425] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:51,429] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:51,429] [INFO] Target genome list was writen to GCF_007828955.1_ASM782895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:51,459] [INFO] Task started: fastANI
[2024-01-24 13:48:51,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f630dc2-a3f0-4722-abba-d8fb06faceb4/GCF_007828955.1_ASM782895v1_genomic.fna.gz --refList GCF_007828955.1_ASM782895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007828955.1_ASM782895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:23,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:23,955] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:23,956] [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_007828955.1	s__Kitasatospora atroaurantiaca	100.0	2620	2623	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_014203705.1	s__Kitasatospora gansuensis	85.2892	1633	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424875.1	s__Kitasatospora sp001424875	85.2151	1585	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.95	99.95	0.99	0.99	2	-
GCF_002943525.1	s__Kitasatospora sp002943525	84.7719	1599	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655955.1	s__Kitasatospora indigofera	84.6748	1615	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648975.1	s__Kitasatospora herbaricolor	84.6215	1618	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	-
GCF_009569385.1	s__Kitasatospora kaniharaensis	84.1989	1432	2623	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	83.9976	1461	2623	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	83.9314	1478	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000961885.1	s__Kitasatospora rubellomurina	83.8483	1422	2623	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	83.8314	1475	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.54	97.86	0.95	0.85	10	-
GCF_000744785.1	s__Kitasatospora azatica	83.8226	1490	2623	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744225.1	s__Kitasatospora mediocidica	83.8172	1426	2623	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	83.6613	1444	2623	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 13:49:23,957] [INFO] GTDB search result was written to GCF_007828955.1_ASM782895v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:23,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:23,961] [INFO] DFAST_QC result json was written to GCF_007828955.1_ASM782895v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:23,962] [INFO] DFAST_QC completed!
[2024-01-24 13:49:23,962] [INFO] Total running time: 0h2m54s