[2024-01-24 13:55:19,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference
[2024-01-24 13:55:20,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,468] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a366843-000b-4e34-bb17-675d1b886eb7/GCF_014655955.1_ASM1465595v1_genomic.fna.gz | prodigal -d GCF_014655955.1_ASM1465595v1_genomic.fna/cds.fna -a GCF_014655955.1_ASM1465595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:45,493] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:45,493] [INFO] Task started: HMMsearch
[2024-01-24 13:55:45,494] [INFO] Running command: hmmsearch --tblout GCF_014655955.1_ASM1465595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/reference_markers.hmm GCF_014655955.1_ASM1465595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:46,008] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:46,009] [INFO] Found 6/6 markers.
[2024-01-24 13:55:46,102] [INFO] Query marker FASTA was written to GCF_014655955.1_ASM1465595v1_genomic.fna/markers.fasta
[2024-01-24 13:55:46,102] [INFO] Task started: Blastn
[2024-01-24 13:55:46,102] [INFO] Running command: blastn -query GCF_014655955.1_ASM1465595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/reference_markers.fasta -out GCF_014655955.1_ASM1465595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:47,535] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:47,538] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:47,539] [INFO] Target genome list was writen to GCF_014655955.1_ASM1465595v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:47,564] [INFO] Task started: fastANI
[2024-01-24 13:55:47,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a366843-000b-4e34-bb17-675d1b886eb7/GCF_014655955.1_ASM1465595v1_genomic.fna.gz --refList GCF_014655955.1_ASM1465595v1_genomic.fna/target_genomes.txt --output GCF_014655955.1_ASM1465595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:28,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:28,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:28,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:28,540] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:28,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:28,540] [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 indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	100.0	3040	3047	95	conclusive
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	94.4677	2610	3047	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	84.5726	1607	3047	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	84.1563	1820	3047	95	below_threshold
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	83.9292	1643	3047	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	83.9199	1656	3047	95	below_threshold
Kitasatospora gansuensis	strain=DSM 44786	GCA_014203705.1	258050	258050	type	True	83.7988	1686	3047	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	83.7722	1455	3047	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	83.3929	1718	3047	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	83.1824	1515	3047	95	below_threshold
Kitasatospora mediocidica	strain=KCTC 9733	GCA_000744225.1	58352	58352	type	True	83.0249	1591	3047	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	82.5938	1496	3047	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	82.3542	1452	3047	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	82.2065	1380	3047	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	78.7763	937	3047	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	77.8691	1194	3047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:28,542] [INFO] DFAST Taxonomy check result was written to GCF_014655955.1_ASM1465595v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:28,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:28,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:28,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/checkm_data
[2024-01-24 13:56:28,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:28,628] [INFO] Task started: CheckM
[2024-01-24 13:56:28,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655955.1_ASM1465595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655955.1_ASM1465595v1_genomic.fna/checkm_input GCF_014655955.1_ASM1465595v1_genomic.fna/checkm_result
[2024-01-24 13:58:22,100] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:22,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,123] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:22,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:22,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655955.1_ASM1465595v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:22,124] [INFO] Task started: Blastn
[2024-01-24 13:58:22,124] [INFO] Running command: blastn -query GCF_014655955.1_ASM1465595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a931c0d-d9b6-4cc2-8be1-5a236c8cd724/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655955.1_ASM1465595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,633] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,638] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:24,638] [INFO] Target genome list was writen to GCF_014655955.1_ASM1465595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:24,709] [INFO] Task started: fastANI
[2024-01-24 13:58:24,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a366843-000b-4e34-bb17-675d1b886eb7/GCF_014655955.1_ASM1465595v1_genomic.fna.gz --refList GCF_014655955.1_ASM1465595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655955.1_ASM1465595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,632] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,632] [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_014655955.1	s__Kitasatospora indigofera	100.0	3040	3047	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_014648975.1	s__Kitasatospora herbaricolor	94.4988	2606	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.20	96.20	0.86	0.86	2	-
GCF_007828955.1	s__Kitasatospora atroaurantiaca	84.5484	1611	3047	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	84.5387	1526	3047	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	84.4023	1726	3047	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	84.1126	1671	3047	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	84.0509	1612	3047	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	83.9796	1645	3047	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	83.9429	1594	3047	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	83.8552	1664	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	99.95	99.95	0.99	0.99	2	-
GCF_014203705.1	s__Kitasatospora gansuensis	83.7931	1686	3047	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	83.6549	1528	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744785.1	s__Kitasatospora azatica	83.1469	1520	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943525.1	s__Kitasatospora sp002943525	83.1233	1654	3047	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	83.056	1584	3047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203855.1	s__Kitasatospora kifunensis	82.5857	1498	3047	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 13:59:05,634] [INFO] GTDB search result was written to GCF_014655955.1_ASM1465595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,638] [INFO] DFAST_QC result json was written to GCF_014655955.1_ASM1465595v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,638] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,638] [INFO] Total running time: 0h3m47s