[2024-01-24 14:03:08,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,466] [INFO] DQC Reference Directory: /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference
[2024-01-24 14:03:09,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,924] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg407ab6ca-1798-4d8c-b7de-56c4dc46daa1/GCF_014649435.1_ASM1464943v1_genomic.fna.gz | prodigal -d GCF_014649435.1_ASM1464943v1_genomic.fna/cds.fna -a GCF_014649435.1_ASM1464943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:34,251] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:34,251] [INFO] Task started: HMMsearch
[2024-01-24 14:03:34,251] [INFO] Running command: hmmsearch --tblout GCF_014649435.1_ASM1464943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/reference_markers.hmm GCF_014649435.1_ASM1464943v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:34,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:34,634] [INFO] Found 6/6 markers.
[2024-01-24 14:03:34,703] [INFO] Query marker FASTA was written to GCF_014649435.1_ASM1464943v1_genomic.fna/markers.fasta
[2024-01-24 14:03:34,703] [INFO] Task started: Blastn
[2024-01-24 14:03:34,703] [INFO] Running command: blastn -query GCF_014649435.1_ASM1464943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/reference_markers.fasta -out GCF_014649435.1_ASM1464943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:36,166] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:36,169] [INFO] Selected 18 target genomes.
[2024-01-24 14:03:36,170] [INFO] Target genome list was writen to GCF_014649435.1_ASM1464943v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:36,181] [INFO] Task started: fastANI
[2024-01-24 14:03:36,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg407ab6ca-1798-4d8c-b7de-56c4dc46daa1/GCF_014649435.1_ASM1464943v1_genomic.fna.gz --refList GCF_014649435.1_ASM1464943v1_genomic.fna/target_genomes.txt --output GCF_014649435.1_ASM1464943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:11,896] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:11,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:11,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:11,913] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:04:11,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:11,913] [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=JCM 4354	GCA_014649435.1	42881	42881	type	True	100.0	2711	2717	95	conclusive
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	99.9235	2453	2717	95	conclusive
Streptomyces gossypiisoli	strain=TRM 44567	GCA_013433285.1	2748864	2748864	type	True	90.8817	1923	2717	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	90.7755	1952	2717	95	below_threshold
Streptomyces spinoverrucosus	strain=NBRC 14228	GCA_006539505.1	284043	284043	type	True	90.6704	1922	2717	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.8942	1721	2717	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3396	1624	2717	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2697	1402	2717	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.2025	1728	2717	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.1898	1435	2717	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.096	1784	2717	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	85.0509	1641	2717	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	85.0313	1635	2717	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	84.8683	1641	2717	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.6813	1664	2717	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	78.5496	1030	2717	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.8971	683	2717	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.7759	545	2717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:11,915] [INFO] DFAST Taxonomy check result was written to GCF_014649435.1_ASM1464943v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:11,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:11,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:11,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/checkm_data
[2024-01-24 14:04:11,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:11,991] [INFO] Task started: CheckM
[2024-01-24 14:04:11,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649435.1_ASM1464943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649435.1_ASM1464943v1_genomic.fna/checkm_input GCF_014649435.1_ASM1464943v1_genomic.fna/checkm_result
[2024-01-24 14:06:02,974] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:02,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:03,001] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:03,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:03,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649435.1_ASM1464943v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:03,002] [INFO] Task started: Blastn
[2024-01-24 14:06:03,002] [INFO] Running command: blastn -query GCF_014649435.1_ASM1464943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga00164b3-c1a1-4846-ba2d-bf779ce422f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649435.1_ASM1464943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:05,414] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:05,418] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:05,419] [INFO] Target genome list was writen to GCF_014649435.1_ASM1464943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:05,431] [INFO] Task started: fastANI
[2024-01-24 14:06:05,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg407ab6ca-1798-4d8c-b7de-56c4dc46daa1/GCF_014649435.1_ASM1464943v1_genomic.fna.gz --refList GCF_014649435.1_ASM1464943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649435.1_ASM1464943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:47,829] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:47,844] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:47,844] [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	99.9316	2452	2717	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	91.0969	1824	2717	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	91.0692	1920	2717	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	90.6509	1925	2717	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	87.7723	1867	2717	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	86.6379	1927	2717	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	86.0734	1665	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000696115.1	s__Streptomyces olindensis	85.7235	1710	2717	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	85.3902	1766	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671715.1	s__Streptomyces sp003671715	85.2795	1658	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.92	0.81	0.81	2	-
GCF_003143935.1	s__Streptomyces sp003143935	85.1014	1810	2717	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	84.8954	1781	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	84.8148	1677	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_000225525.1	s__Streptomyces zinciresistens	84.7516	1518	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143855.1	s__Streptomyces sp003143855	84.5492	1569	2717	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_004342105.1	s__Streptomyces sp004342105	84.4577	1661	2717	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	84.1956	1784	2717	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 14:06:47,846] [INFO] GTDB search result was written to GCF_014649435.1_ASM1464943v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:47,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:47,851] [INFO] DFAST_QC result json was written to GCF_014649435.1_ASM1464943v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:47,852] [INFO] DFAST_QC completed!
[2024-01-24 14:06:47,852] [INFO] Total running time: 0h3m39s