[2024-01-25 19:57:35,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:35,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:35,545] [INFO] DQC Reference Directory: /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference
[2024-01-25 19:57:36,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:36,696] [INFO] Task started: Prodigal
[2024-01-25 19:57:36,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a48daa1-12b9-49cb-a0c1-ed3890528f5f/GCF_016860545.1_ASM1686054v1_genomic.fna.gz | prodigal -d GCF_016860545.1_ASM1686054v1_genomic.fna/cds.fna -a GCF_016860545.1_ASM1686054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:06,739] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:06,740] [INFO] Task started: HMMsearch
[2024-01-25 19:58:06,740] [INFO] Running command: hmmsearch --tblout GCF_016860545.1_ASM1686054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/reference_markers.hmm GCF_016860545.1_ASM1686054v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:07,104] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:07,105] [INFO] Found 6/6 markers.
[2024-01-25 19:58:07,171] [INFO] Query marker FASTA was written to GCF_016860545.1_ASM1686054v1_genomic.fna/markers.fasta
[2024-01-25 19:58:07,171] [INFO] Task started: Blastn
[2024-01-25 19:58:07,171] [INFO] Running command: blastn -query GCF_016860545.1_ASM1686054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/reference_markers.fasta -out GCF_016860545.1_ASM1686054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:08,387] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:08,397] [INFO] Selected 14 target genomes.
[2024-01-25 19:58:08,397] [INFO] Target genome list was writen to GCF_016860545.1_ASM1686054v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:08,411] [INFO] Task started: fastANI
[2024-01-25 19:58:08,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a48daa1-12b9-49cb-a0c1-ed3890528f5f/GCF_016860545.1_ASM1686054v1_genomic.fna.gz --refList GCF_016860545.1_ASM1686054v1_genomic.fna/target_genomes.txt --output GCF_016860545.1_ASM1686054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:43,755] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:43,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:43,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:43,765] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:58:43,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:43,765] [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 asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	100.0	2943	2943	95	conclusive
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	99.9825	2892	2943	95	conclusive
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	88.1854	2157	2943	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	87.8962	2025	2943	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	87.1875	2145	2943	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.5765	1748	2943	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.0538	1976	2943	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.8586	1877	2943	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	84.7602	1597	2943	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	84.7072	1857	2943	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.4982	1426	2943	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.4951	1752	2943	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.7527	1888	2943	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.2342	1817	2943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:43,767] [INFO] DFAST Taxonomy check result was written to GCF_016860545.1_ASM1686054v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:43,767] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:43,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:43,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/checkm_data
[2024-01-25 19:58:43,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:43,848] [INFO] Task started: CheckM
[2024-01-25 19:58:43,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016860545.1_ASM1686054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016860545.1_ASM1686054v1_genomic.fna/checkm_input GCF_016860545.1_ASM1686054v1_genomic.fna/checkm_result
[2024-01-25 20:01:32,181] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:32,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:32,203] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:32,204] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:32,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016860545.1_ASM1686054v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:32,205] [INFO] Task started: Blastn
[2024-01-25 20:01:32,205] [INFO] Running command: blastn -query GCF_016860545.1_ASM1686054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc81f42f9-d88b-4c89-a7d3-492d0e0f56cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_016860545.1_ASM1686054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:34,300] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:34,303] [INFO] Selected 13 target genomes.
[2024-01-25 20:01:34,303] [INFO] Target genome list was writen to GCF_016860545.1_ASM1686054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:34,336] [INFO] Task started: fastANI
[2024-01-25 20:01:34,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a48daa1-12b9-49cb-a0c1-ed3890528f5f/GCF_016860545.1_ASM1686054v1_genomic.fna.gz --refList GCF_016860545.1_ASM1686054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016860545.1_ASM1686054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:07,699] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:07,708] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:07,708] [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_016860545.1	s__Streptomyces asoensis	100.0	2942	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	conclusive
GCF_013085465.1	s__Streptomyces cacaoi_A	90.4695	2318	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001298545.1	s__Streptomyces sp001298545	90.3725	2348	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.23	95.13	0.87	0.84	4	-
GCF_001184025.1	s__Streptomyces sp001184025	90.2961	2197	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.49	98.49	0.84	0.84	2	-
GCF_900129855.1	s__Streptomyces sp900129855	88.7983	2036	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.68	99.68	0.97	0.97	2	-
GCF_900110755.1	s__Streptomyces sp900110755	88.2757	2014	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112535.1	s__Streptomyces rishiriensis	88.2166	2154	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746365.1	s__Streptomyces sp001746365	88.1988	2140	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428885.1	s__Streptomyces sp001428885	87.8893	2124	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003032475.1	s__Streptomyces sp003032475	87.7215	2089	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648915.1	s__Streptomyces phaeofaciens	87.196	2143	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010548375.1	s__Streptomyces sp010548375	84.8579	1968	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	84.5678	1947	2943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:07,715] [INFO] GTDB search result was written to GCF_016860545.1_ASM1686054v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:07,716] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:07,719] [INFO] DFAST_QC result json was written to GCF_016860545.1_ASM1686054v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:07,719] [INFO] DFAST_QC completed!
[2024-01-25 20:02:07,719] [INFO] Total running time: 0h4m32s