[2024-01-24 13:46:25,729] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference
[2024-01-24 13:46:26,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,962] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg139d2e2a-46b7-4758-b53a-e115ff1f3a15/GCF_014650575.1_ASM1465057v1_genomic.fna.gz | prodigal -d GCF_014650575.1_ASM1465057v1_genomic.fna/cds.fna -a GCF_014650575.1_ASM1465057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:50,089] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:50,089] [INFO] Task started: HMMsearch
[2024-01-24 13:46:50,090] [INFO] Running command: hmmsearch --tblout GCF_014650575.1_ASM1465057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/reference_markers.hmm GCF_014650575.1_ASM1465057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:50,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:50,456] [INFO] Found 6/6 markers.
[2024-01-24 13:46:50,521] [INFO] Query marker FASTA was written to GCF_014650575.1_ASM1465057v1_genomic.fna/markers.fasta
[2024-01-24 13:46:50,521] [INFO] Task started: Blastn
[2024-01-24 13:46:50,522] [INFO] Running command: blastn -query GCF_014650575.1_ASM1465057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/reference_markers.fasta -out GCF_014650575.1_ASM1465057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,883] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:51,884] [INFO] Target genome list was writen to GCF_014650575.1_ASM1465057v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:51,897] [INFO] Task started: fastANI
[2024-01-24 13:46:51,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg139d2e2a-46b7-4758-b53a-e115ff1f3a15/GCF_014650575.1_ASM1465057v1_genomic.fna.gz --refList GCF_014650575.1_ASM1465057v1_genomic.fna/target_genomes.txt --output GCF_014650575.1_ASM1465057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:35,943] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:35,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:35,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:35,966] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:35,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:35,967] [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 naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	100.0	2563	2566	95	conclusive
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	94.5258	2184	2566	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	87.7645	1820	2566	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	87.6524	1626	2566	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	87.6514	1590	2566	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	85.7442	1484	2566	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.5726	1630	2566	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	85.5713	1767	2566	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	85.4384	1742	2566	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.4235	1645	2566	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.4014	1648	2566	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.3871	1771	2566	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.3426	1632	2566	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.3161	1674	2566	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	85.3157	1331	2566	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.2462	1763	2566	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	85.2444	1753	2566	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	84.5071	1586	2566	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4321	1557	2566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:35,969] [INFO] DFAST Taxonomy check result was written to GCF_014650575.1_ASM1465057v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:35,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:35,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:35,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/checkm_data
[2024-01-24 13:47:35,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:36,047] [INFO] Task started: CheckM
[2024-01-24 13:47:36,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650575.1_ASM1465057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650575.1_ASM1465057v1_genomic.fna/checkm_input GCF_014650575.1_ASM1465057v1_genomic.fna/checkm_result
[2024-01-24 13:49:18,080] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:18,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:18,121] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:18,121] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:18,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650575.1_ASM1465057v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:18,122] [INFO] Task started: Blastn
[2024-01-24 13:49:18,122] [INFO] Running command: blastn -query GCF_014650575.1_ASM1465057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg757cf6bd-6f2b-4fd3-9090-d0e1d73c8a24/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650575.1_ASM1465057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:20,565] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:20,570] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:20,571] [INFO] Target genome list was writen to GCF_014650575.1_ASM1465057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:20,602] [INFO] Task started: fastANI
[2024-01-24 13:49:20,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg139d2e2a-46b7-4758-b53a-e115ff1f3a15/GCF_014650575.1_ASM1465057v1_genomic.fna.gz --refList GCF_014650575.1_ASM1465057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650575.1_ASM1465057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:55,396] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:55,412] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:55,413] [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_014650575.1	s__Streptomyces naganishii	100.0	2563	2566	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_014650655.1	s__Streptomyces anandii	94.5266	2184	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	87.7679	1819	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	87.6538	1623	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	87.3091	1761	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_013364255.1	s__Streptomyces seoulensis_A	87.1332	1748	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720185.1	s__Streptomyces sp000720185	87.059	1738	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654495.1	s__Streptomyces sp001654495	87.0147	1695	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.91	96.91	0.92	0.92	2	-
GCF_001514215.1	s__Streptomyces bungoensis	85.5492	1771	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513965.1	s__Streptomyces cellostaticus	85.437	1763	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	85.3017	1675	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649495.1	s__Streptomyces filipinensis	85.2167	1749	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.80	96.80	0.89	0.89	2	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.9224	1720	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	83.9682	1631	2566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:55,418] [INFO] GTDB search result was written to GCF_014650575.1_ASM1465057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:55,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:55,432] [INFO] DFAST_QC result json was written to GCF_014650575.1_ASM1465057v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:55,432] [INFO] DFAST_QC completed!
[2024-01-24 13:49:55,432] [INFO] Total running time: 0h3m30s