[2024-01-24 15:19:52,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference
[2024-01-24 15:19:53,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,915] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,915] [INFO] Running command: gunzip -c /var/lib/cwl/stgbeb735ee-ef96-4f42-bf7c-db81f1bb1adf/GCF_017676345.1_ASM1767634v1_genomic.fna.gz | prodigal -d GCF_017676345.1_ASM1767634v1_genomic.fna/cds.fna -a GCF_017676345.1_ASM1767634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:17,620] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:17,621] [INFO] Task started: HMMsearch
[2024-01-24 15:20:17,621] [INFO] Running command: hmmsearch --tblout GCF_017676345.1_ASM1767634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/reference_markers.hmm GCF_017676345.1_ASM1767634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:18,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:18,087] [INFO] Found 6/6 markers.
[2024-01-24 15:20:18,159] [INFO] Query marker FASTA was written to GCF_017676345.1_ASM1767634v1_genomic.fna/markers.fasta
[2024-01-24 15:20:18,160] [INFO] Task started: Blastn
[2024-01-24 15:20:18,160] [INFO] Running command: blastn -query GCF_017676345.1_ASM1767634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/reference_markers.fasta -out GCF_017676345.1_ASM1767634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:19,501] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:19,505] [INFO] Selected 13 target genomes.
[2024-01-24 15:20:19,505] [INFO] Target genome list was writen to GCF_017676345.1_ASM1767634v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:19,510] [INFO] Task started: fastANI
[2024-01-24 15:20:19,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb735ee-ef96-4f42-bf7c-db81f1bb1adf/GCF_017676345.1_ASM1767634v1_genomic.fna.gz --refList GCF_017676345.1_ASM1767634v1_genomic.fna/target_genomes.txt --output GCF_017676345.1_ASM1767634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:43,400] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:43,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:43,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:43,416] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:43,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:43,417] [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 smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	100.0	2658	2661	95	conclusive
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	89.1101	1920	2661	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	88.6471	1767	2661	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	87.5327	1772	2661	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	87.436	1772	2661	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	85.2324	1701	2661	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	85.2022	1663	2661	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	82.5736	1239	2661	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	80.3695	921	2661	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	80.3603	1078	2661	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.3209	1223	2661	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.3127	1245	2661	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.2118	1227	2661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:43,418] [INFO] DFAST Taxonomy check result was written to GCF_017676345.1_ASM1767634v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:43,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:43,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:43,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/checkm_data
[2024-01-24 15:20:43,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:43,496] [INFO] Task started: CheckM
[2024-01-24 15:20:43,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017676345.1_ASM1767634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017676345.1_ASM1767634v1_genomic.fna/checkm_input GCF_017676345.1_ASM1767634v1_genomic.fna/checkm_result
[2024-01-24 15:22:39,143] [INFO] Task succeeded: CheckM
[2024-01-24 15:22:39,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:22:39,170] [INFO] ===== Completeness check finished =====
[2024-01-24 15:22:39,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:22:39,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017676345.1_ASM1767634v1_genomic.fna/markers.fasta)
[2024-01-24 15:22:39,171] [INFO] Task started: Blastn
[2024-01-24 15:22:39,171] [INFO] Running command: blastn -query GCF_017676345.1_ASM1767634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56251846-9f3f-4c0d-9452-d1aaa7e8aa96/dqc_reference/reference_markers_gtdb.fasta -out GCF_017676345.1_ASM1767634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:22:41,135] [INFO] Task succeeded: Blastn
[2024-01-24 15:22:41,139] [INFO] Selected 7 target genomes.
[2024-01-24 15:22:41,140] [INFO] Target genome list was writen to GCF_017676345.1_ASM1767634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:22:41,145] [INFO] Task started: fastANI
[2024-01-24 15:22:41,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb735ee-ef96-4f42-bf7c-db81f1bb1adf/GCF_017676345.1_ASM1767634v1_genomic.fna.gz --refList GCF_017676345.1_ASM1767634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017676345.1_ASM1767634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:22:55,807] [INFO] Task succeeded: fastANI
[2024-01-24 15:22:55,820] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:22:55,820] [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_017676345.1	s__Streptomyces smyrnaeus	100.0	2658	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.11	97.08	0.90	0.88	5	conclusive
GCF_017676385.1	s__Streptomyces sp017676385	89.1092	1921	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017676365.1	s__Streptomyces oryzae	88.6515	1767	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111245.1	s__Streptomyces qinglanensis	87.4325	1772	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000424765.1	s__Streptomyces sp000424765	87.2638	1779	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.13	98.98	0.93	0.92	5	-
GCF_013302895.1	s__Streptomyces chlorinus	86.0254	1790	2661	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726235.1	s__Streptomyces sp012726235	81.6108	1217	2661	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 15:22:55,822] [INFO] GTDB search result was written to GCF_017676345.1_ASM1767634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:22:55,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:22:55,825] [INFO] DFAST_QC result json was written to GCF_017676345.1_ASM1767634v1_genomic.fna/dqc_result.json
[2024-01-24 15:22:55,826] [INFO] DFAST_QC completed!
[2024-01-24 15:22:55,826] [INFO] Total running time: 0h3m3s