[2024-01-24 15:27:20,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,822] [INFO] DQC Reference Directory: /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference
[2024-01-24 15:27:23,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,292] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,293] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbac06b8-1f93-41d2-82a8-8b5b53e6e290/GCF_027497475.1_ASM2749747v1_genomic.fna.gz | prodigal -d GCF_027497475.1_ASM2749747v1_genomic.fna/cds.fna -a GCF_027497475.1_ASM2749747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:51,719] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:51,720] [INFO] Task started: HMMsearch
[2024-01-24 15:27:51,720] [INFO] Running command: hmmsearch --tblout GCF_027497475.1_ASM2749747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/reference_markers.hmm GCF_027497475.1_ASM2749747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:52,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:52,131] [INFO] Found 6/6 markers.
[2024-01-24 15:27:52,199] [INFO] Query marker FASTA was written to GCF_027497475.1_ASM2749747v1_genomic.fna/markers.fasta
[2024-01-24 15:27:52,199] [INFO] Task started: Blastn
[2024-01-24 15:27:52,199] [INFO] Running command: blastn -query GCF_027497475.1_ASM2749747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/reference_markers.fasta -out GCF_027497475.1_ASM2749747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:53,523] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:53,526] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:53,526] [INFO] Target genome list was writen to GCF_027497475.1_ASM2749747v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:53,535] [INFO] Task started: fastANI
[2024-01-24 15:27:53,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbac06b8-1f93-41d2-82a8-8b5b53e6e290/GCF_027497475.1_ASM2749747v1_genomic.fna.gz --refList GCF_027497475.1_ASM2749747v1_genomic.fna/target_genomes.txt --output GCF_027497475.1_ASM2749747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:30,125] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:30,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:30,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:30,146] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:30,146] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:30,146] [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 libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	99.9947	3041	3067	95	conclusive
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	99.9935	3021	3067	95	conclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	93.0197	2427	3067	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	92.7256	2304	3067	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	92.2781	2192	3067	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	90.6533	2289	3067	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	90.597	2172	3067	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	89.7873	2182	3067	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	89.7583	1973	3067	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	88.9576	2000	3067	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.5522	1640	3067	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.183	1325	3067	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.667	1658	3067	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.543	1729	3067	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.5424	1740	3067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:30,148] [INFO] DFAST Taxonomy check result was written to GCF_027497475.1_ASM2749747v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:30,149] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:30,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:30,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/checkm_data
[2024-01-24 15:28:30,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:30,236] [INFO] Task started: CheckM
[2024-01-24 15:28:30,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027497475.1_ASM2749747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027497475.1_ASM2749747v1_genomic.fna/checkm_input GCF_027497475.1_ASM2749747v1_genomic.fna/checkm_result
[2024-01-24 15:30:49,438] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:49,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:49,463] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:49,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:49,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027497475.1_ASM2749747v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:49,464] [INFO] Task started: Blastn
[2024-01-24 15:30:49,465] [INFO] Running command: blastn -query GCF_027497475.1_ASM2749747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0aae2ec-4e09-4868-9361-1be97c6b1399/dqc_reference/reference_markers_gtdb.fasta -out GCF_027497475.1_ASM2749747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:51,528] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:51,535] [INFO] Selected 10 target genomes.
[2024-01-24 15:30:51,535] [INFO] Target genome list was writen to GCF_027497475.1_ASM2749747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:51,544] [INFO] Task started: fastANI
[2024-01-24 15:30:51,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbac06b8-1f93-41d2-82a8-8b5b53e6e290/GCF_027497475.1_ASM2749747v1_genomic.fna.gz --refList GCF_027497475.1_ASM2749747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027497475.1_ASM2749747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:31:15,704] [INFO] Task succeeded: fastANI
[2024-01-24 15:31:15,714] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:31:15,714] [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_009811595.1	s__Streptomyces libani	99.9947	3042	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	conclusive
GCF_008704855.1	s__Streptomyces platensis	92.768	2369	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_009811635.1	s__Streptomyces tubercidicus	92.2677	2193	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	90.6131	2170	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	90.093	2268	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003389455.1	s__Streptomyces inhibens	89.8382	2036	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.8201	2106	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_009176265.1	s__Streptomyces angustmyceticus	89.7586	2162	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.7381	1976	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_014646275.1	s__Streptomyces kronopolitis	88.9362	2003	3067	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 15:31:15,716] [INFO] GTDB search result was written to GCF_027497475.1_ASM2749747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:31:15,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:31:15,720] [INFO] DFAST_QC result json was written to GCF_027497475.1_ASM2749747v1_genomic.fna/dqc_result.json
[2024-01-24 15:31:15,720] [INFO] DFAST_QC completed!
[2024-01-24 15:31:15,720] [INFO] Total running time: 0h3m55s