[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference
[2024-01-24 12:00:39,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,374] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a4e17c0-0a5b-415d-b7e1-fd69bdffed83/GCF_015160875.1_ASM1516087v1_genomic.fna.gz | prodigal -d GCF_015160875.1_ASM1516087v1_genomic.fna/cds.fna -a GCF_015160875.1_ASM1516087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:01:00,367] [INFO] Task succeeded: Prodigal
[2024-01-24 12:01:00,367] [INFO] Task started: HMMsearch
[2024-01-24 12:01:00,368] [INFO] Running command: hmmsearch --tblout GCF_015160875.1_ASM1516087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/reference_markers.hmm GCF_015160875.1_ASM1516087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:00,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:00,690] [INFO] Found 6/6 markers.
[2024-01-24 12:01:00,749] [INFO] Query marker FASTA was written to GCF_015160875.1_ASM1516087v1_genomic.fna/markers.fasta
[2024-01-24 12:01:00,749] [INFO] Task started: Blastn
[2024-01-24 12:01:00,749] [INFO] Running command: blastn -query GCF_015160875.1_ASM1516087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/reference_markers.fasta -out GCF_015160875.1_ASM1516087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:02,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:02,074] [INFO] Selected 13 target genomes.
[2024-01-24 12:01:02,075] [INFO] Target genome list was writen to GCF_015160875.1_ASM1516087v1_genomic.fna/target_genomes.txt
[2024-01-24 12:01:02,082] [INFO] Task started: fastANI
[2024-01-24 12:01:02,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4e17c0-0a5b-415d-b7e1-fd69bdffed83/GCF_015160875.1_ASM1516087v1_genomic.fna.gz --refList GCF_015160875.1_ASM1516087v1_genomic.fna/target_genomes.txt --output GCF_015160875.1_ASM1516087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:28,875] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:28,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:28,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:28,888] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:01:28,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:28,889] [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 chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	100.0	2494	2494	95	conclusive
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	99.9645	2444	2494	95	conclusive
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	91.1874	1874	2494	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	91.0138	1890	2494	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	91.0086	1852	2494	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.0512	1666	2494	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.4011	1368	2494	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3683	1620	2494	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.3595	1388	2494	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.3013	1741	2494	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	85.1711	1614	2494	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.132	1596	2494	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.7754	1626	2494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:28,891] [INFO] DFAST Taxonomy check result was written to GCF_015160875.1_ASM1516087v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:28,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:28,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:28,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/checkm_data
[2024-01-24 12:01:28,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:28,967] [INFO] Task started: CheckM
[2024-01-24 12:01:28,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015160875.1_ASM1516087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015160875.1_ASM1516087v1_genomic.fna/checkm_input GCF_015160875.1_ASM1516087v1_genomic.fna/checkm_result
[2024-01-24 12:03:26,556] [INFO] Task succeeded: CheckM
[2024-01-24 12:03:26,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:03:26,583] [INFO] ===== Completeness check finished =====
[2024-01-24 12:03:26,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:03:26,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015160875.1_ASM1516087v1_genomic.fna/markers.fasta)
[2024-01-24 12:03:26,584] [INFO] Task started: Blastn
[2024-01-24 12:03:26,585] [INFO] Running command: blastn -query GCF_015160875.1_ASM1516087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745ff3d4-6a25-4526-8ef5-01993e971f0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_015160875.1_ASM1516087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:03:28,729] [INFO] Task succeeded: Blastn
[2024-01-24 12:03:28,733] [INFO] Selected 13 target genomes.
[2024-01-24 12:03:28,733] [INFO] Target genome list was writen to GCF_015160875.1_ASM1516087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:03:28,754] [INFO] Task started: fastANI
[2024-01-24 12:03:28,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4e17c0-0a5b-415d-b7e1-fd69bdffed83/GCF_015160875.1_ASM1516087v1_genomic.fna.gz --refList GCF_015160875.1_ASM1516087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015160875.1_ASM1516087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:03:57,120] [INFO] Task succeeded: fastANI
[2024-01-24 12:03:57,138] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:03:57,139] [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_015160875.1	s__Streptomyces chromofuscus	100.0	2494	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	conclusive
GCF_019219825.1	s__Streptomyces sp019219825	91.3303	1804	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015712165.1	s__Streptomyces spinoverrucosus_A	91.3024	1907	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	90.9996	1855	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_004187715.1	s__Streptomyces sp004187715	87.9044	1819	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261055.1	s__Streptomyces cadmiisoli	86.9703	1825	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.22	99.22	0.88	0.88	2	-
GCF_000761215.1	s__Streptomyces glaucescens	86.2674	1651	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	85.6557	1738	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	85.4108	1730	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484565.1	s__Streptomyces sp001484565	85.2442	1741	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225525.1	s__Streptomyces zinciresistens	84.8957	1475	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342105.1	s__Streptomyces sp004342105	84.6604	1609	2494	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814875.1	s__Streptomyces sp003814875	84.5102	1723	2494	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 12:03:57,141] [INFO] GTDB search result was written to GCF_015160875.1_ASM1516087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:03:57,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:03:57,146] [INFO] DFAST_QC result json was written to GCF_015160875.1_ASM1516087v1_genomic.fna/dqc_result.json
[2024-01-24 12:03:57,147] [INFO] DFAST_QC completed!
[2024-01-24 12:03:57,147] [INFO] Total running time: 0h3m20s