[2024-01-24 13:10:18,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:18,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:18,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference
[2024-01-24 13:10:20,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,216] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg133387af-55f0-4104-b53a-49ed9214c531/GCF_020521295.1_ASM2052129v1_genomic.fna.gz | prodigal -d GCF_020521295.1_ASM2052129v1_genomic.fna/cds.fna -a GCF_020521295.1_ASM2052129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:46,223] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:46,223] [INFO] Task started: HMMsearch
[2024-01-24 13:10:46,224] [INFO] Running command: hmmsearch --tblout GCF_020521295.1_ASM2052129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/reference_markers.hmm GCF_020521295.1_ASM2052129v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:46,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:46,652] [INFO] Found 6/6 markers.
[2024-01-24 13:10:46,730] [INFO] Query marker FASTA was written to GCF_020521295.1_ASM2052129v1_genomic.fna/markers.fasta
[2024-01-24 13:10:46,730] [INFO] Task started: Blastn
[2024-01-24 13:10:46,730] [INFO] Running command: blastn -query GCF_020521295.1_ASM2052129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/reference_markers.fasta -out GCF_020521295.1_ASM2052129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:48,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:48,170] [INFO] Selected 18 target genomes.
[2024-01-24 13:10:48,170] [INFO] Target genome list was writen to GCF_020521295.1_ASM2052129v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:48,179] [INFO] Task started: fastANI
[2024-01-24 13:10:48,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg133387af-55f0-4104-b53a-49ed9214c531/GCF_020521295.1_ASM2052129v1_genomic.fna.gz --refList GCF_020521295.1_ASM2052129v1_genomic.fna/target_genomes.txt --output GCF_020521295.1_ASM2052129v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:25,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:25,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:25,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:25,818] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:11:25,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:11:25,818] [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
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	100.0	2935	2961	95	conclusive
Streptomyces violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	99.9079	2616	2961	95	conclusive
Streptomyces xanthochromogenes	strain=JCM 4612	GCA_014650455.1	67384	67384	type	True	89.9398	2030	2961	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	85.3258	1737	2961	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.1487	1423	2961	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	83.0742	1433	2961	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.8492	1463	2961	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.7986	1487	2961	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	82.4876	1438	2961	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.296	1448	2961	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	82.2513	1415	2961	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	82.187	1469	2961	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	82.0806	1218	2961	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	81.7618	1092	2961	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.5761	1431	2961	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.5017	1421	2961	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.2349	1304	2961	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	76.3167	522	2961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:25,820] [INFO] DFAST Taxonomy check result was written to GCF_020521295.1_ASM2052129v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:25,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:25,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:25,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/checkm_data
[2024-01-24 13:11:25,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:25,907] [INFO] Task started: CheckM
[2024-01-24 13:11:25,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020521295.1_ASM2052129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020521295.1_ASM2052129v1_genomic.fna/checkm_input GCF_020521295.1_ASM2052129v1_genomic.fna/checkm_result
[2024-01-24 13:12:56,530] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:56,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:56,557] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:56,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:56,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020521295.1_ASM2052129v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:56,558] [INFO] Task started: Blastn
[2024-01-24 13:12:56,558] [INFO] Running command: blastn -query GCF_020521295.1_ASM2052129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2281de0d-5a31-436a-97ab-ab3b50e5cc2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_020521295.1_ASM2052129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:58,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:58,816] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:58,816] [INFO] Target genome list was writen to GCF_020521295.1_ASM2052129v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:58,844] [INFO] Task started: fastANI
[2024-01-24 13:12:58,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg133387af-55f0-4104-b53a-49ed9214c531/GCF_020521295.1_ASM2052129v1_genomic.fna.gz --refList GCF_020521295.1_ASM2052129v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020521295.1_ASM2052129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:22,106] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:22,121] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:22,121] [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_014649955.1	s__Streptomyces violascens	99.9079	2616	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001279695.1	s__Streptomyces sp001279695	93.6739	2222	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324565.1	s__Streptomyces sp003324565	90.8511	2160	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650455.1	s__Streptomyces xanthochromogenes	89.9654	2027	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	97.90	0.92	0.90	3	-
GCF_002803085.1	s__Streptomyces sp002803085	89.9138	1977	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627815.1	s__Streptomyces hundungensis	89.6067	1956	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	85.3421	1734	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_001653515.1	s__Streptomyces sp001653515	85.1271	1471	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700515.1	s__Streptomyces lushanensis	81.7148	1100	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	76.6879	410	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302585.1	s__Kibdelosporangium phytohabitans	76.304	526	2961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:22,123] [INFO] GTDB search result was written to GCF_020521295.1_ASM2052129v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:22,124] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:22,127] [INFO] DFAST_QC result json was written to GCF_020521295.1_ASM2052129v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:22,127] [INFO] DFAST_QC completed!
[2024-01-24 13:13:22,127] [INFO] Total running time: 0h3m3s