[2024-01-24 14:31:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,266] [INFO] DQC Reference Directory: /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,103] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a121b73-ec97-4845-a5e8-38b954c883a2/GCF_002154555.1_ASM215455v1_genomic.fna.gz | prodigal -d GCF_002154555.1_ASM215455v1_genomic.fna/cds.fna -a GCF_002154555.1_ASM215455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:19,515] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:19,516] [INFO] Task started: HMMsearch
[2024-01-24 14:31:19,516] [INFO] Running command: hmmsearch --tblout GCF_002154555.1_ASM215455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/reference_markers.hmm GCF_002154555.1_ASM215455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:19,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:19,968] [INFO] Found 6/6 markers.
[2024-01-24 14:31:20,056] [INFO] Query marker FASTA was written to GCF_002154555.1_ASM215455v1_genomic.fna/markers.fasta
[2024-01-24 14:31:20,056] [INFO] Task started: Blastn
[2024-01-24 14:31:20,056] [INFO] Running command: blastn -query GCF_002154555.1_ASM215455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/reference_markers.fasta -out GCF_002154555.1_ASM215455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:21,322] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:21,325] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:21,325] [INFO] Target genome list was writen to GCF_002154555.1_ASM215455v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:21,329] [INFO] Task started: fastANI
[2024-01-24 14:31:21,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a121b73-ec97-4845-a5e8-38b954c883a2/GCF_002154555.1_ASM215455v1_genomic.fna.gz --refList GCF_002154555.1_ASM215455v1_genomic.fna/target_genomes.txt --output GCF_002154555.1_ASM215455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:41,591] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:41,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:41,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:41,600] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:31:41,600] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:31:41,600] [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 murinus	strain=NRRL B-2286	GCA_002154555.1	33900	33900	type	True	100.0	2133	2163	95	inconclusive
Streptomyces griseofuscus	strain=DSM 40191	GCA_014673495.1	146922	146922	type	True	97.003	1897	2163	95	inconclusive
Streptomyces griseofuscus	strain=NRRL B-5429	GCA_000718315.1	146922	146922	type	True	96.9887	1881	2163	95	inconclusive
Streptomyces malaysiense	strain=MUSC 136	GCA_000980885.2	1428626	1428626	type	True	93.5788	1693	2163	95	below_threshold
Streptomyces misionensis	strain=DSM 40306	GCA_900104815.1	67331	67331	type	True	89.9332	1643	2163	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	86.7699	1463	2163	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	86.4712	1453	2163	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.5675	1123	2163	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.4877	1420	2163	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.1225	1156	2163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:41,602] [INFO] DFAST Taxonomy check result was written to GCF_002154555.1_ASM215455v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:41,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:41,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:41,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/checkm_data
[2024-01-24 14:31:41,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:41,679] [INFO] Task started: CheckM
[2024-01-24 14:31:41,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002154555.1_ASM215455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002154555.1_ASM215455v1_genomic.fna/checkm_input GCF_002154555.1_ASM215455v1_genomic.fna/checkm_result
[2024-01-24 14:32:42,759] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:42,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:42,778] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:42,778] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:42,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002154555.1_ASM215455v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:42,778] [INFO] Task started: Blastn
[2024-01-24 14:32:42,778] [INFO] Running command: blastn -query GCF_002154555.1_ASM215455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga77b8b5d-2cd8-49f0-be54-dca682dc7181/dqc_reference/reference_markers_gtdb.fasta -out GCF_002154555.1_ASM215455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:44,826] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:44,828] [INFO] Selected 6 target genomes.
[2024-01-24 14:32:44,828] [INFO] Target genome list was writen to GCF_002154555.1_ASM215455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:44,832] [INFO] Task started: fastANI
[2024-01-24 14:32:44,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a121b73-ec97-4845-a5e8-38b954c883a2/GCF_002154555.1_ASM215455v1_genomic.fna.gz --refList GCF_002154555.1_ASM215455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002154555.1_ASM215455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:57,036] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:57,041] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:32:57,041] [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_002154555.1	s__Streptomyces murinus	100.0	2133	2163	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	97.0065	97.48	97.10	0.91	0.89	7	inconclusive
GCF_014673495.1	s__Streptomyces griseofuscus	97.007	1896	2163	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	97.0065	98.75	98.11	0.94	0.90	10	inconclusive
GCF_007679425.1	s__Streptomyces incarnatus_A	94.6966	1745	2163	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.00	0.97	0.94	3	-
GCF_009650765.1	s__Streptomyces sp003259585	94.4326	1841	2163	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.79	98.74	0.95	0.93	5	-
GCF_000980885.2	s__Streptomyces malaysiense	93.59	1692	2163	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896895.1	s__Streptomyces misionensis_A	90.0795	1574	2163	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 14:32:57,043] [INFO] GTDB search result was written to GCF_002154555.1_ASM215455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:57,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:57,045] [INFO] DFAST_QC result json was written to GCF_002154555.1_ASM215455v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:57,045] [INFO] DFAST_QC completed!
[2024-01-24 14:32:57,045] [INFO] Total running time: 0h1m57s