[2024-01-24 11:51:24,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference
[2024-01-24 11:51:26,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,083] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg28bf4b71-d15b-4b40-93f6-c09fae1d2173/GCF_013870515.1_ASM1387051v1_genomic.fna.gz | prodigal -d GCF_013870515.1_ASM1387051v1_genomic.fna/cds.fna -a GCF_013870515.1_ASM1387051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:43,130] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:43,130] [INFO] Task started: HMMsearch
[2024-01-24 11:51:43,130] [INFO] Running command: hmmsearch --tblout GCF_013870515.1_ASM1387051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/reference_markers.hmm GCF_013870515.1_ASM1387051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:43,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:43,467] [INFO] Found 6/6 markers.
[2024-01-24 11:51:43,530] [INFO] Query marker FASTA was written to GCF_013870515.1_ASM1387051v1_genomic.fna/markers.fasta
[2024-01-24 11:51:43,530] [INFO] Task started: Blastn
[2024-01-24 11:51:43,530] [INFO] Running command: blastn -query GCF_013870515.1_ASM1387051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/reference_markers.fasta -out GCF_013870515.1_ASM1387051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:44,807] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:44,812] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:44,813] [INFO] Target genome list was writen to GCF_013870515.1_ASM1387051v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:44,821] [INFO] Task started: fastANI
[2024-01-24 11:51:44,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bf4b71-d15b-4b40-93f6-c09fae1d2173/GCF_013870515.1_ASM1387051v1_genomic.fna.gz --refList GCF_013870515.1_ASM1387051v1_genomic.fna/target_genomes.txt --output GCF_013870515.1_ASM1387051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:11,585] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:11,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:11,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:11,600] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:11,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:11,601] [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 albidus (ex Kaewkla and Franco 2021)	strain=CAP215	GCA_013870515.1	722709	722709	type	True	100.0	1944	1966	95	conclusive
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	84.5061	1415	1966	95	below_threshold
Streptomyces bathyalis	strain=ASO4wet	GCA_015910445.1	2710756	2710756	type	True	84.4231	1507	1966	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	80.9828	863	1966	95	below_threshold
Streptomyces oryzae	strain=S16-07	GCA_017676365.1	1434886	1434886	type	True	80.9216	925	1966	95	below_threshold
Streptomyces reniochalinae	strain=LHW50302	GCA_003323735.1	2250578	2250578	type	True	80.8699	972	1966	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	80.8143	930	1966	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	80.81	929	1966	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	80.6736	988	1966	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	80.6347	801	1966	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	80.5894	797	1966	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	80.4407	806	1966	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	80.146	838	1966	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.1116	914	1966	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.0497	846	1966	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.0219	942	1966	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	80.0123	900	1966	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	79.9769	922	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:11,602] [INFO] DFAST Taxonomy check result was written to GCF_013870515.1_ASM1387051v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:11,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:11,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:11,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/checkm_data
[2024-01-24 11:52:11,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:11,672] [INFO] Task started: CheckM
[2024-01-24 11:52:11,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013870515.1_ASM1387051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013870515.1_ASM1387051v1_genomic.fna/checkm_input GCF_013870515.1_ASM1387051v1_genomic.fna/checkm_result
[2024-01-24 11:53:31,980] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:31,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:32,009] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:32,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:32,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013870515.1_ASM1387051v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:32,010] [INFO] Task started: Blastn
[2024-01-24 11:53:32,011] [INFO] Running command: blastn -query GCF_013870515.1_ASM1387051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1791a8d-e0e2-46e4-82c9-a02f569d8831/dqc_reference/reference_markers_gtdb.fasta -out GCF_013870515.1_ASM1387051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:33,999] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:34,004] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:34,005] [INFO] Target genome list was writen to GCF_013870515.1_ASM1387051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:34,014] [INFO] Task started: fastANI
[2024-01-24 11:53:34,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg28bf4b71-d15b-4b40-93f6-c09fae1d2173/GCF_013870515.1_ASM1387051v1_genomic.fna.gz --refList GCF_013870515.1_ASM1387051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013870515.1_ASM1387051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:53,242] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:53,258] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:53,259] [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_013870515.1	s__Streptomyces albidus	100.0	1944	1966	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_000424965.1	s__Streptomyces sp000424965	85.4914	1426	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751365.1	s__Streptomyces abyssalis	84.5764	1427	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.91	99.91	0.99	0.99	2	-
GCF_014645895.1	s__Streptomyces daqingensis	84.5152	1414	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.92	0.92	3	-
GCF_014204855.1	s__Streptomyces haliclonae	84.501	1389	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426165.1	s__Streptomyces sp000426165	84.4978	1465	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015910445.1	s__Streptomyces bathyalis	84.4343	1505	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001751255.1	s__Streptomyces nanshensis_A	84.2787	1255	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.85	97.85	0.86	0.86	2	-
GCF_012726265.1	s__Streptomyces sp012726265	84.1165	1403	1966	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	81.7015	1006	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003323735.1	s__Streptomyces reniochalinae	80.8755	972	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718985.1	s__Streptomyces megasporus	80.6345	801	1966	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	80.6006	795	1966	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 11:53:53,260] [INFO] GTDB search result was written to GCF_013870515.1_ASM1387051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:53,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:53,266] [INFO] DFAST_QC result json was written to GCF_013870515.1_ASM1387051v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:53,266] [INFO] DFAST_QC completed!
[2024-01-24 11:53:53,266] [INFO] Total running time: 0h2m29s