[2024-01-24 13:57:16,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:16,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:16,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference
[2024-01-24 13:57:18,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:18,421] [INFO] Task started: Prodigal
[2024-01-24 13:57:18,422] [INFO] Running command: gunzip -c /var/lib/cwl/stga5e17c86-d27a-4c32-a7ea-60cdad9fc23e/GCF_000725545.1_Doro.v1.0_genomic.fna.gz | prodigal -d GCF_000725545.1_Doro.v1.0_genomic.fna/cds.fna -a GCF_000725545.1_Doro.v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:40,254] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:40,255] [INFO] Task started: HMMsearch
[2024-01-24 13:57:40,255] [INFO] Running command: hmmsearch --tblout GCF_000725545.1_Doro.v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/reference_markers.hmm GCF_000725545.1_Doro.v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:40,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:40,655] [INFO] Found 6/6 markers.
[2024-01-24 13:57:40,754] [INFO] Query marker FASTA was written to GCF_000725545.1_Doro.v1.0_genomic.fna/markers.fasta
[2024-01-24 13:57:40,756] [INFO] Task started: Blastn
[2024-01-24 13:57:40,757] [INFO] Running command: blastn -query GCF_000725545.1_Doro.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/reference_markers.fasta -out GCF_000725545.1_Doro.v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:42,184] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:42,187] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:42,187] [INFO] Target genome list was writen to GCF_000725545.1_Doro.v1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:42,198] [INFO] Task started: fastANI
[2024-01-24 13:57:42,198] [INFO] Running command: fastANI --query /var/lib/cwl/stga5e17c86-d27a-4c32-a7ea-60cdad9fc23e/GCF_000725545.1_Doro.v1.0_genomic.fna.gz --refList GCF_000725545.1_Doro.v1.0_genomic.fna/target_genomes.txt --output GCF_000725545.1_Doro.v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:16,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:16,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:16,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:16,517] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:16,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:16,517] [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 exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	100.0	2574	2577	95	conclusive
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	99.9901	2565	2577	95	conclusive
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	90.3731	1947	2577	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	90.2766	1938	2577	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_000253235.1	54571	54571	type	True	90.2237	1953	2577	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	90.0583	1511	2577	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.7531	1954	2577	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.6643	1968	2577	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	89.4584	2000	2577	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	89.4269	1970	2577	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.3881	1927	2577	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	89.2808	1956	2577	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.601	1421	2577	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.4719	1380	2577	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.2474	1248	2577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:16,519] [INFO] DFAST Taxonomy check result was written to GCF_000725545.1_Doro.v1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:58:16,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:16,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:16,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/checkm_data
[2024-01-24 13:58:16,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:16,593] [INFO] Task started: CheckM
[2024-01-24 13:58:16,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000725545.1_Doro.v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000725545.1_Doro.v1.0_genomic.fna/checkm_input GCF_000725545.1_Doro.v1.0_genomic.fna/checkm_result
[2024-01-24 13:59:51,024] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:51,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:51,046] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:51,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:51,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000725545.1_Doro.v1.0_genomic.fna/markers.fasta)
[2024-01-24 13:59:51,048] [INFO] Task started: Blastn
[2024-01-24 13:59:51,048] [INFO] Running command: blastn -query GCF_000725545.1_Doro.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ddfc033-5a2a-481d-a693-24ef66117af9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000725545.1_Doro.v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:53,254] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:53,258] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:53,259] [INFO] Target genome list was writen to GCF_000725545.1_Doro.v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:53,268] [INFO] Task started: fastANI
[2024-01-24 13:59:53,269] [INFO] Running command: fastANI --query /var/lib/cwl/stga5e17c86-d27a-4c32-a7ea-60cdad9fc23e/GCF_000725545.1_Doro.v1.0_genomic.fna.gz --refList GCF_000725545.1_Doro.v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000725545.1_Doro.v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:20,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:20,662] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:20,663] [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_000725545.1	s__Streptomyces exfoliatus	100.0	2574	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	conclusive
GCA_000717735.1	s__Streptomyces griseoluteus_A	96.3087	2204	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_001905665.1	s__Streptomyces sp001905665	90.7664	1996	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656215.1	s__Streptomyces zaomyceticus	90.3798	1946	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008639165.1	s__Streptomyces venezuelae	90.2695	1939	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCF_001418135.1	s__Streptomyces aureus_A	90.2496	1705	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	90.2176	1896	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905825.1	s__Streptomyces sp001905825	89.9128	1984	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_014451325.1	s__Streptomyces sp014451325	89.8561	1377	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.7868	1949	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_006539185.1	s__Streptomyces gardneri	89.4677	1965	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_008042145.1	s__Streptomyces sp008042145	89.3922	1787	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386135.1	s__Streptomyces sp003386135	89.3525	1939	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:20,665] [INFO] GTDB search result was written to GCF_000725545.1_Doro.v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:20,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:20,671] [INFO] DFAST_QC result json was written to GCF_000725545.1_Doro.v1.0_genomic.fna/dqc_result.json
[2024-01-24 14:00:20,672] [INFO] DFAST_QC completed!
[2024-01-24 14:00:20,672] [INFO] Total running time: 0h3m4s