[2024-01-24 13:18:27,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,376] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference
[2024-01-24 13:18:28,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,732] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgab47874e-ab4c-4bbb-a804-2c5efa66f11d/GCF_014649075.1_ASM1464907v1_genomic.fna.gz | prodigal -d GCF_014649075.1_ASM1464907v1_genomic.fna/cds.fna -a GCF_014649075.1_ASM1464907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:53,059] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:53,059] [INFO] Task started: HMMsearch
[2024-01-24 13:18:53,060] [INFO] Running command: hmmsearch --tblout GCF_014649075.1_ASM1464907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/reference_markers.hmm GCF_014649075.1_ASM1464907v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:53,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:53,457] [INFO] Found 6/6 markers.
[2024-01-24 13:18:53,527] [INFO] Query marker FASTA was written to GCF_014649075.1_ASM1464907v1_genomic.fna/markers.fasta
[2024-01-24 13:18:53,527] [INFO] Task started: Blastn
[2024-01-24 13:18:53,528] [INFO] Running command: blastn -query GCF_014649075.1_ASM1464907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/reference_markers.fasta -out GCF_014649075.1_ASM1464907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,829] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,835] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:54,835] [INFO] Target genome list was writen to GCF_014649075.1_ASM1464907v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:54,841] [INFO] Task started: fastANI
[2024-01-24 13:18:54,841] [INFO] Running command: fastANI --query /var/lib/cwl/stgab47874e-ab4c-4bbb-a804-2c5efa66f11d/GCF_014649075.1_ASM1464907v1_genomic.fna.gz --refList GCF_014649075.1_ASM1464907v1_genomic.fna/target_genomes.txt --output GCF_014649075.1_ASM1464907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:28,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:28,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:28,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:28,424] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:28,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:28,424] [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=JCM 4185	GCA_014649075.1	249586	249586	type	True	100.0	2933	2934	95	conclusive
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	99.9938	2892	2934	95	conclusive
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	88.3067	2136	2934	95	below_threshold
Streptomyces humidus	strain=JCM 4386	GCA_014649655.1	52259	52259	type	True	87.8926	2040	2934	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	87.1573	2144	2934	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	86.672	1734	2934	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.9575	1987	2934	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9037	1878	2934	95	below_threshold
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	84.8604	1575	2934	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.6356	1712	2934	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.5709	1400	2934	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	84.51	1848	2934	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.8	1861	2934	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	83.2696	1785	2934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:28,426] [INFO] DFAST Taxonomy check result was written to GCF_014649075.1_ASM1464907v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:28,427] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:28,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:28,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/checkm_data
[2024-01-24 13:19:28,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:28,534] [INFO] Task started: CheckM
[2024-01-24 13:19:28,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649075.1_ASM1464907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649075.1_ASM1464907v1_genomic.fna/checkm_input GCF_014649075.1_ASM1464907v1_genomic.fna/checkm_result
[2024-01-24 13:21:26,158] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:26,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:26,197] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:26,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:26,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649075.1_ASM1464907v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:26,198] [INFO] Task started: Blastn
[2024-01-24 13:21:26,198] [INFO] Running command: blastn -query GCF_014649075.1_ASM1464907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277b187e-3cc2-473f-92a6-1ac848255175/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649075.1_ASM1464907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:28,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:28,453] [INFO] Selected 13 target genomes.
[2024-01-24 13:21:28,453] [INFO] Target genome list was writen to GCF_014649075.1_ASM1464907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:28,466] [INFO] Task started: fastANI
[2024-01-24 13:21:28,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgab47874e-ab4c-4bbb-a804-2c5efa66f11d/GCF_014649075.1_ASM1464907v1_genomic.fna.gz --refList GCF_014649075.1_ASM1464907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649075.1_ASM1464907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:01,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:01,839] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:01,839] [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	99.9938	2892	2934	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	90.4149	2313	2934	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	90.327	2338	2934	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	90.2527	2208	2934	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	88.7358	2033	2934	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	88.3329	2009	2934	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	88.3067	2135	2934	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	88.1515	2116	2934	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	87.9105	2117	2934	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	87.7153	2066	2934	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	87.173	2141	2934	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	84.7462	1975	2934	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	84.4999	1932	2934	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 13:22:01,841] [INFO] GTDB search result was written to GCF_014649075.1_ASM1464907v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:01,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:01,845] [INFO] DFAST_QC result json was written to GCF_014649075.1_ASM1464907v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:01,845] [INFO] DFAST_QC completed!
[2024-01-24 13:22:01,845] [INFO] Total running time: 0h3m34s