[2024-01-24 15:18:22,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:22,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:22,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference
[2024-01-24 15:18:25,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,005] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d8c6fe1-87d6-4d59-8ca3-2839c311d9bf/GCF_009811555.1_ASM981155v1_genomic.fna.gz | prodigal -d GCF_009811555.1_ASM981155v1_genomic.fna/cds.fna -a GCF_009811555.1_ASM981155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:57,279] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:57,280] [INFO] Task started: HMMsearch
[2024-01-24 15:18:57,280] [INFO] Running command: hmmsearch --tblout GCF_009811555.1_ASM981155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/reference_markers.hmm GCF_009811555.1_ASM981155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:57,738] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:57,739] [INFO] Found 6/6 markers.
[2024-01-24 15:18:57,822] [INFO] Query marker FASTA was written to GCF_009811555.1_ASM981155v1_genomic.fna/markers.fasta
[2024-01-24 15:18:57,823] [INFO] Task started: Blastn
[2024-01-24 15:18:57,823] [INFO] Running command: blastn -query GCF_009811555.1_ASM981155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/reference_markers.fasta -out GCF_009811555.1_ASM981155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:59,179] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:59,183] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:59,184] [INFO] Target genome list was writen to GCF_009811555.1_ASM981155v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:59,202] [INFO] Task started: fastANI
[2024-01-24 15:18:59,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8c6fe1-87d6-4d59-8ca3-2839c311d9bf/GCF_009811555.1_ASM981155v1_genomic.fna.gz --refList GCF_009811555.1_ASM981155v1_genomic.fna/target_genomes.txt --output GCF_009811555.1_ASM981155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:39,279] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:39,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:39,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:39,294] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:39,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:39,295] [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 caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	100.0	3036	3045	95	conclusive
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	92.5412	2315	3045	95	below_threshold
Streptomyces angustmyceticus	strain=NBRC 3934	GCA_009176265.1	285578	285578	type	True	92.4675	2293	3045	95	below_threshold
Streptomyces angustmyceticus	strain=NRRL B-2347	GCA_002154415.1	285578	285578	type	True	92.3565	1739	3045	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	91.5375	2349	3045	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	91.5077	2240	3045	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	89.8241	2187	3045	95	below_threshold
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	89.8154	2170	3045	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	89.798	2162	3045	95	below_threshold
Streptomyces glebosus	strain=JCM 4954	GCA_014656235.1	249580	249580	type	True	89.7865	2150	3045	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	89.7766	2115	3045	95	below_threshold
Streptomyces tubercidicus	strain=NBRC 13090	GCA_009811635.1	47759	47759	type	True	89.5609	2028	3045	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	89.0712	2013	3045	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.5454	1645	3045	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4627	1315	3045	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.7547	1746	3045	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.7518	1722	3045	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.673	1687	3045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,296] [INFO] DFAST Taxonomy check result was written to GCF_009811555.1_ASM981155v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:39,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:39,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:39,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/checkm_data
[2024-01-24 15:19:39,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:39,385] [INFO] Task started: CheckM
[2024-01-24 15:19:39,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009811555.1_ASM981155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009811555.1_ASM981155v1_genomic.fna/checkm_input GCF_009811555.1_ASM981155v1_genomic.fna/checkm_result
[2024-01-24 15:22:02,539] [INFO] Task succeeded: CheckM
[2024-01-24 15:22:02,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 26.04%
Strain heterogeneity: 77.78%
--------------------------------------------------------------------------------
[2024-01-24 15:22:02,565] [INFO] ===== Completeness check finished =====
[2024-01-24 15:22:02,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:22:02,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009811555.1_ASM981155v1_genomic.fna/markers.fasta)
[2024-01-24 15:22:02,566] [INFO] Task started: Blastn
[2024-01-24 15:22:02,566] [INFO] Running command: blastn -query GCF_009811555.1_ASM981155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c15b166-7dc4-44b6-9816-d7d0afaeb557/dqc_reference/reference_markers_gtdb.fasta -out GCF_009811555.1_ASM981155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:22:04,620] [INFO] Task succeeded: Blastn
[2024-01-24 15:22:04,623] [INFO] Selected 9 target genomes.
[2024-01-24 15:22:04,624] [INFO] Target genome list was writen to GCF_009811555.1_ASM981155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:22:04,630] [INFO] Task started: fastANI
[2024-01-24 15:22:04,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8c6fe1-87d6-4d59-8ca3-2839c311d9bf/GCF_009811555.1_ASM981155v1_genomic.fna.gz --refList GCF_009811555.1_ASM981155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009811555.1_ASM981155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:26,058] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:26,076] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:26,077] [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_009811555.1	s__Streptomyces caniferus	100.0	3035	3045	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_009176265.1	s__Streptomyces angustmyceticus	92.4416	2297	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_900187385.1	s__Streptomyces sp900187385	91.8955	2230	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	91.6318	2191	3045	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	91.4948	2241	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_008704855.1	s__Streptomyces platensis	89.8132	2160	3045	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	89.5527	2028	3045	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.4307	1916	3045	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	89.0795	2012	3045	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 15:22:26,079] [INFO] GTDB search result was written to GCF_009811555.1_ASM981155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:26,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:26,084] [INFO] DFAST_QC result json was written to GCF_009811555.1_ASM981155v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:26,085] [INFO] DFAST_QC completed!
[2024-01-24 15:22:26,085] [INFO] Total running time: 0h4m3s