[2024-01-24 12:22:48,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference
[2024-01-24 12:22:49,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,206] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf89549f-19bc-4734-ad78-32884c999567/GCF_003594885.1_ASM359488v1_genomic.fna.gz | prodigal -d GCF_003594885.1_ASM359488v1_genomic.fna/cds.fna -a GCF_003594885.1_ASM359488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:58,134] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:58,135] [INFO] Task started: HMMsearch
[2024-01-24 12:22:58,135] [INFO] Running command: hmmsearch --tblout GCF_003594885.1_ASM359488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/reference_markers.hmm GCF_003594885.1_ASM359488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:58,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:58,345] [INFO] Found 6/6 markers.
[2024-01-24 12:22:58,377] [INFO] Query marker FASTA was written to GCF_003594885.1_ASM359488v1_genomic.fna/markers.fasta
[2024-01-24 12:22:58,378] [INFO] Task started: Blastn
[2024-01-24 12:22:58,378] [INFO] Running command: blastn -query GCF_003594885.1_ASM359488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/reference_markers.fasta -out GCF_003594885.1_ASM359488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:59,829] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:59,833] [INFO] Selected 29 target genomes.
[2024-01-24 12:22:59,833] [INFO] Target genome list was writen to GCF_003594885.1_ASM359488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:59,886] [INFO] Task started: fastANI
[2024-01-24 12:22:59,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf89549f-19bc-4734-ad78-32884c999567/GCF_003594885.1_ASM359488v1_genomic.fna.gz --refList GCF_003594885.1_ASM359488v1_genomic.fna/target_genomes.txt --output GCF_003594885.1_ASM359488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:36,435] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:36,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:36,451] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:36,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:36,452] [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
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	78.4828	604	1341	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	78.2681	626	1341	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	78.1611	615	1341	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	78.0925	658	1341	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	77.3929	486	1341	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.2699	391	1341	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	77.1637	639	1341	95	below_threshold
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	76.9587	498	1341	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	76.9386	508	1341	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	76.9211	547	1341	95	below_threshold
Streptomyces fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	76.7978	561	1341	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	76.7713	456	1341	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.7567	568	1341	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	76.7217	606	1341	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	76.6976	597	1341	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	76.6927	477	1341	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	76.6856	584	1341	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	76.6773	583	1341	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	76.6194	610	1341	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	76.6134	553	1341	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	76.593	681	1341	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	76.5845	675	1341	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	76.5677	613	1341	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	76.5417	614	1341	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	76.4803	582	1341	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.45	729	1341	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.447	714	1341	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	76.3265	707	1341	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	76.3257	693	1341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,453] [INFO] DFAST Taxonomy check result was written to GCF_003594885.1_ASM359488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:36,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:36,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:36,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/checkm_data
[2024-01-24 12:23:36,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:36,496] [INFO] Task started: CheckM
[2024-01-24 12:23:36,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003594885.1_ASM359488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003594885.1_ASM359488v1_genomic.fna/checkm_input GCF_003594885.1_ASM359488v1_genomic.fna/checkm_result
[2024-01-24 12:24:22,476] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:22,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:22,491] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:22,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:22,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003594885.1_ASM359488v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:22,492] [INFO] Task started: Blastn
[2024-01-24 12:24:22,492] [INFO] Running command: blastn -query GCF_003594885.1_ASM359488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e5d326c-bfdd-419a-9746-0411c7df1920/dqc_reference/reference_markers_gtdb.fasta -out GCF_003594885.1_ASM359488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:25,047] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:25,049] [INFO] Selected 23 target genomes.
[2024-01-24 12:24:25,049] [INFO] Target genome list was writen to GCF_003594885.1_ASM359488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:25,074] [INFO] Task started: fastANI
[2024-01-24 12:24:25,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf89549f-19bc-4734-ad78-32884c999567/GCF_003594885.1_ASM359488v1_genomic.fna.gz --refList GCF_003594885.1_ASM359488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003594885.1_ASM359488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:53,451] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:53,464] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:53,464] [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_003594885.1	s__Vallicoccus soli	100.0	1341	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003634695.1	s__Motilibacter peucedani	78.4301	611	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	78.2204	634	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250635.1	s__Motilibacter_A deserti	78.1562	616	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250645.1	s__Motilibacter_A aurantiacus	78.1399	650	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	77.4041	349	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	77.3816	489	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	77.3334	626	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	77.1744	636	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	76.9235	490	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	76.9085	492	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565425.1	s__Actinotalea sp017565425	76.8144	433	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112515.1	s__Streptomyces fragilis	76.7778	565	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	76.7465	578	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093975.1	s__Nonomuraea rubra_A	76.737	603	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	76.7059	574	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	76.6587	590	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	76.6278	714	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	76.6263	609	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719335.1	s__Streptomyces sp000719335	76.6099	598	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	76.5684	742	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	76.4197	722	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552135.1	s__Spirillospora chibensis	76.3302	693	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:53,465] [INFO] GTDB search result was written to GCF_003594885.1_ASM359488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:53,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:53,470] [INFO] DFAST_QC result json was written to GCF_003594885.1_ASM359488v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:53,470] [INFO] DFAST_QC completed!
[2024-01-24 12:24:53,470] [INFO] Total running time: 0h2m5s