[2024-01-24 14:05:59,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:59,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:59,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference
[2024-01-24 14:06:00,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:00,327] [INFO] Task started: Prodigal
[2024-01-24 14:06:00,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca1c1a0-684a-4272-ab45-08f596c64d6b/GCF_006334995.2_ASM633499v2_genomic.fna.gz | prodigal -d GCF_006334995.2_ASM633499v2_genomic.fna/cds.fna -a GCF_006334995.2_ASM633499v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:22,073] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:22,074] [INFO] Task started: HMMsearch
[2024-01-24 14:06:22,074] [INFO] Running command: hmmsearch --tblout GCF_006334995.2_ASM633499v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/reference_markers.hmm GCF_006334995.2_ASM633499v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:22,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:22,357] [INFO] Found 6/6 markers.
[2024-01-24 14:06:22,412] [INFO] Query marker FASTA was written to GCF_006334995.2_ASM633499v2_genomic.fna/markers.fasta
[2024-01-24 14:06:22,412] [INFO] Task started: Blastn
[2024-01-24 14:06:22,412] [INFO] Running command: blastn -query GCF_006334995.2_ASM633499v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/reference_markers.fasta -out GCF_006334995.2_ASM633499v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,845] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:23,846] [INFO] Target genome list was writen to GCF_006334995.2_ASM633499v2_genomic.fna/target_genomes.txt
[2024-01-24 14:06:23,855] [INFO] Task started: fastANI
[2024-01-24 14:06:23,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca1c1a0-684a-4272-ab45-08f596c64d6b/GCF_006334995.2_ASM633499v2_genomic.fna.gz --refList GCF_006334995.2_ASM633499v2_genomic.fna/target_genomes.txt --output GCF_006334995.2_ASM633499v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:54,246] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:54,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:54,265] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:54,265] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:54,265] [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 mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	100.0	2372	2376	95	inconclusive
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	95.2551	1752	2376	95	inconclusive
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	87.2969	1591	2376	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	87.1211	1607	2376	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.5445	1186	2376	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.472	1070	2376	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.3495	1299	2376	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.2007	1249	2376	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	80.8591	1313	2376	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.4077	881	2376	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.2267	1016	2376	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	78.9446	823	2376	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	78.7354	730	2376	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	78.7062	1111	2376	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.5265	1034	2376	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	78.4706	1092	2376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,268] [INFO] DFAST Taxonomy check result was written to GCF_006334995.2_ASM633499v2_genomic.fna/tc_result.tsv
[2024-01-24 14:06:54,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:54,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:54,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/checkm_data
[2024-01-24 14:06:54,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:54,336] [INFO] Task started: CheckM
[2024-01-24 14:06:54,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006334995.2_ASM633499v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006334995.2_ASM633499v2_genomic.fna/checkm_input GCF_006334995.2_ASM633499v2_genomic.fna/checkm_result
[2024-01-24 14:08:32,565] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:32,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:32,591] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:32,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:32,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006334995.2_ASM633499v2_genomic.fna/markers.fasta)
[2024-01-24 14:08:32,592] [INFO] Task started: Blastn
[2024-01-24 14:08:32,592] [INFO] Running command: blastn -query GCF_006334995.2_ASM633499v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6499750a-acde-4067-90eb-70a73f5c665a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006334995.2_ASM633499v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:35,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:35,071] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:35,071] [INFO] Target genome list was writen to GCF_006334995.2_ASM633499v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:35,079] [INFO] Task started: fastANI
[2024-01-24 14:08:35,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca1c1a0-684a-4272-ab45-08f596c64d6b/GCF_006334995.2_ASM633499v2_genomic.fna.gz --refList GCF_006334995.2_ASM633499v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006334995.2_ASM633499v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:00,173] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:00,184] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:00,185] [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_003696235.1	s__Streptomyces triticirhizae	95.2709	1751	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	conclusive
GCF_900230195.1	s__Streptomyces zhaozhouensis	87.2983	1589	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	87.0533	1617	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	84.6509	1657	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	81.7217	1144	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	81.5111	1214	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.4891	1065	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.4777	1199	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	81.3379	1299	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003311645.1	s__Streptomyces sp003311645	81.2093	1232	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116145.1	s__Streptomyces harbinensis	81.0558	1129	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_003626535.1	s__Streptomyces hoynatensis	80.9602	1296	2376	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:00,188] [INFO] GTDB search result was written to GCF_006334995.2_ASM633499v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:00,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:00,193] [INFO] DFAST_QC result json was written to GCF_006334995.2_ASM633499v2_genomic.fna/dqc_result.json
[2024-01-24 14:09:00,193] [INFO] DFAST_QC completed!
[2024-01-24 14:09:00,194] [INFO] Total running time: 0h3m1s