[2024-01-24 11:20:49,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,821] [INFO] DQC Reference Directory: /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference
[2024-01-24 11:20:51,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,055] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,055] [INFO] Running command: gunzip -c /var/lib/cwl/stga764f831-7db7-440f-b051-f2502682d2d9/GCF_003258605.2_ASM325860v2_genomic.fna.gz | prodigal -d GCF_003258605.2_ASM325860v2_genomic.fna/cds.fna -a GCF_003258605.2_ASM325860v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:13,292] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:13,292] [INFO] Task started: HMMsearch
[2024-01-24 11:21:13,293] [INFO] Running command: hmmsearch --tblout GCF_003258605.2_ASM325860v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/reference_markers.hmm GCF_003258605.2_ASM325860v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:13,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:13,614] [INFO] Found 6/6 markers.
[2024-01-24 11:21:13,667] [INFO] Query marker FASTA was written to GCF_003258605.2_ASM325860v2_genomic.fna/markers.fasta
[2024-01-24 11:21:13,668] [INFO] Task started: Blastn
[2024-01-24 11:21:13,668] [INFO] Running command: blastn -query GCF_003258605.2_ASM325860v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/reference_markers.fasta -out GCF_003258605.2_ASM325860v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:15,025] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:15,030] [INFO] Selected 19 target genomes.
[2024-01-24 11:21:15,030] [INFO] Target genome list was writen to GCF_003258605.2_ASM325860v2_genomic.fna/target_genomes.txt
[2024-01-24 11:21:15,074] [INFO] Task started: fastANI
[2024-01-24 11:21:15,074] [INFO] Running command: fastANI --query /var/lib/cwl/stga764f831-7db7-440f-b051-f2502682d2d9/GCF_003258605.2_ASM325860v2_genomic.fna.gz --refList GCF_003258605.2_ASM325860v2_genomic.fna/target_genomes.txt --output GCF_003258605.2_ASM325860v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:52,029] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:52,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:52,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:52,049] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:52,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:52,049] [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
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	100.0	2363	2363	95	conclusive
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	85.8394	1266	2363	95	below_threshold
Kitasatospora atroaurantiaca	strain=DSM 41649	GCA_007828955.1	285545	285545	type	True	81.6781	1190	2363	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	81.3696	1116	2363	95	below_threshold
Kitasatospora azatica	strain=KCTC 9699	GCA_000744785.1	58347	58347	type	True	81.3626	1176	2363	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	81.2971	1292	2363	95	below_threshold
Kitasatospora indigofera	strain=JCM 4646	GCA_014655955.1	67307	67307	type	True	81.1278	1296	2363	95	below_threshold
Kitasatospora kifunensis	strain=DSM 41654	GCA_014203855.1	58351	58351	type	True	80.9961	1173	2363	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	80.9397	1252	2363	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	80.9384	1240	2363	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	80.9339	1101	2363	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	80.5377	1115	2363	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	80.5098	1142	2363	95	below_threshold
Streptacidiphilus fuscans	strain=NEAU-YB345	GCA_015690355.1	2789292	2789292	type	True	80.0714	1017	2363	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	79.8506	1000	2363	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.7394	1091	2363	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	79.6428	1090	2363	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	79.3058	976	2363	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	79.126	833	2363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:52,051] [INFO] DFAST Taxonomy check result was written to GCF_003258605.2_ASM325860v2_genomic.fna/tc_result.tsv
[2024-01-24 11:21:52,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:52,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:52,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/checkm_data
[2024-01-24 11:21:52,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:52,126] [INFO] Task started: CheckM
[2024-01-24 11:21:52,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258605.2_ASM325860v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258605.2_ASM325860v2_genomic.fna/checkm_input GCF_003258605.2_ASM325860v2_genomic.fna/checkm_result
[2024-01-24 11:23:45,370] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:45,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:45,397] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:45,398] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:45,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258605.2_ASM325860v2_genomic.fna/markers.fasta)
[2024-01-24 11:23:45,398] [INFO] Task started: Blastn
[2024-01-24 11:23:45,399] [INFO] Running command: blastn -query GCF_003258605.2_ASM325860v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga7f8d363-317b-4ff7-ae84-bf76d1e94049/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258605.2_ASM325860v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:47,475] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:47,479] [INFO] Selected 19 target genomes.
[2024-01-24 11:23:47,480] [INFO] Target genome list was writen to GCF_003258605.2_ASM325860v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:47,532] [INFO] Task started: fastANI
[2024-01-24 11:23:47,533] [INFO] Running command: fastANI --query /var/lib/cwl/stga764f831-7db7-440f-b051-f2502682d2d9/GCF_003258605.2_ASM325860v2_genomic.fna.gz --refList GCF_003258605.2_ASM325860v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003258605.2_ASM325860v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:24,914] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:24,932] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:24,932] [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_003258605.2	s__Streptomyces_D bronchialis	100.0	2363	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001418575.1	s__Streptomyces_D griseoplanus	85.8065	1270	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828955.1	s__Kitasatospora atroaurantiaca	81.7244	1184	2363	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	81.6276	1139	2363	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	81.2917	1157	2363	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	81.1393	1265	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	98.73	98.73	0.93	0.93	2	-
GCA_019192735.1	s__Kitasatospora aureofaciens_A	81.134	1169	2363	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	81.1261	1300	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846355.1	s__Kitasatospora sp002846355	81.0614	1153	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	-
GCF_003205575.1	s__Kitasatospora tateyamensis	81.0511	1126	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084125.1	s__Streptacidiphilus sp014084125	81.0256	1138	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719695.1	s__Kitasatospora sp000719695	80.9597	1210	2363	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	80.7928	1238	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365705.1	s__Streptacidiphilus sp004365705	80.675	1148	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787775.1	s__Streptacidiphilus carbonis	80.5083	1119	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719095.1	s__Streptacidiphilus jeojiense	80.5075	1154	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744815.1	s__Streptacidiphilus_A oryzae	80.0954	1128	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690355.1	s__Streptacidiphilus fuscans	80.029	1025	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	79.6248	1093	2363	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:24,934] [INFO] GTDB search result was written to GCF_003258605.2_ASM325860v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:24,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:24,939] [INFO] DFAST_QC result json was written to GCF_003258605.2_ASM325860v2_genomic.fna/dqc_result.json
[2024-01-24 11:24:24,939] [INFO] DFAST_QC completed!
[2024-01-24 11:24:24,939] [INFO] Total running time: 0h3m35s