[2023-06-17 07:53:23,525] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:53:23,527] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:53:23,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference
[2023-06-17 07:53:24,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:53:24,821] [INFO] Task started: Prodigal
[2023-06-17 07:53:24,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg940b0422-3b55-416a-aa95-571828eb6678/GCA_013333735.2_ASM1333373v2_genomic.fna.gz | prodigal -d GCA_013333735.2_ASM1333373v2_genomic.fna/cds.fna -a GCA_013333735.2_ASM1333373v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:53:32,907] [INFO] Task succeeded: Prodigal
[2023-06-17 07:53:32,908] [INFO] Task started: HMMsearch
[2023-06-17 07:53:32,908] [INFO] Running command: hmmsearch --tblout GCA_013333735.2_ASM1333373v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/reference_markers.hmm GCA_013333735.2_ASM1333373v2_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:53:33,180] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:53:33,182] [INFO] Found 6/6 markers.
[2023-06-17 07:53:33,214] [INFO] Query marker FASTA was written to GCA_013333735.2_ASM1333373v2_genomic.fna/markers.fasta
[2023-06-17 07:53:33,214] [INFO] Task started: Blastn
[2023-06-17 07:53:33,215] [INFO] Running command: blastn -query GCA_013333735.2_ASM1333373v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/reference_markers.fasta -out GCA_013333735.2_ASM1333373v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:53:34,027] [INFO] Task succeeded: Blastn
[2023-06-17 07:53:34,031] [INFO] Selected 16 target genomes.
[2023-06-17 07:53:34,031] [INFO] Target genome list was writen to GCA_013333735.2_ASM1333373v2_genomic.fna/target_genomes.txt
[2023-06-17 07:53:34,033] [INFO] Task started: fastANI
[2023-06-17 07:53:34,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg940b0422-3b55-416a-aa95-571828eb6678/GCA_013333735.2_ASM1333373v2_genomic.fna.gz --refList GCA_013333735.2_ASM1333373v2_genomic.fna/target_genomes.txt --output GCA_013333735.2_ASM1333373v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:53:44,279] [INFO] Task succeeded: fastANI
[2023-06-17 07:53:44,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:53:44,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:53:44,298] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 07:53:44,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 07:53:44,299] [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
Arachnia rubra	strain=SK-1	GCA_019973735.1	1547448	1547448	type	True	99.2103	881	906	95	conclusive
Arachnia propionica	strain=NCTC12967	GCA_900637725.1	1750	1750	type	True	82.1757	571	906	95	below_threshold
Arachnia propionica	strain=NBRC 14587	GCA_001592325.1	1750	1750	type	True	82.1575	569	906	95	below_threshold
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	81.9653	554	906	95	below_threshold
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	77.8925	205	906	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	77.6834	200	906	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	77.5283	186	906	95	below_threshold
Tessaracoccus antarcticus	strain=JDX10	GCA_003688855.1	2479848	2479848	type	True	77.4403	170	906	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	77.086	128	906	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	76.2519	81	906	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	76.2483	98	906	95	below_threshold
Naumannella halotolerans	strain=DSM 24323	GCA_004364645.1	993414	993414	type	True	76.2232	83	906	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.1051	55	906	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.0265	92	906	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	75.943	56	906	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	75.8825	56	906	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:53:44,301] [INFO] DFAST Taxonomy check result was written to GCA_013333735.2_ASM1333373v2_genomic.fna/tc_result.tsv
[2023-06-17 07:53:44,302] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:53:44,302] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:53:44,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/checkm_data
[2023-06-17 07:53:44,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:53:44,335] [INFO] Task started: CheckM
[2023-06-17 07:53:44,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013333735.2_ASM1333373v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013333735.2_ASM1333373v2_genomic.fna/checkm_input GCA_013333735.2_ASM1333373v2_genomic.fna/checkm_result
[2023-06-17 07:54:13,355] [INFO] Task succeeded: CheckM
[2023-06-17 07:54:13,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:54:13,378] [INFO] ===== Completeness check finished =====
[2023-06-17 07:54:13,379] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:54:13,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013333735.2_ASM1333373v2_genomic.fna/markers.fasta)
[2023-06-17 07:54:13,379] [INFO] Task started: Blastn
[2023-06-17 07:54:13,380] [INFO] Running command: blastn -query GCA_013333735.2_ASM1333373v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg63154776-12b9-4317-a55e-61b4ecdc3f32/dqc_reference/reference_markers_gtdb.fasta -out GCA_013333735.2_ASM1333373v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:54:14,468] [INFO] Task succeeded: Blastn
[2023-06-17 07:54:14,473] [INFO] Selected 11 target genomes.
[2023-06-17 07:54:14,473] [INFO] Target genome list was writen to GCA_013333735.2_ASM1333373v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:54:14,479] [INFO] Task started: fastANI
[2023-06-17 07:54:14,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg940b0422-3b55-416a-aa95-571828eb6678/GCA_013333735.2_ASM1333373v2_genomic.fna.gz --refList GCA_013333735.2_ASM1333373v2_genomic.fna/target_genomes_gtdb.txt --output GCA_013333735.2_ASM1333373v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:54:22,263] [INFO] Task succeeded: fastANI
[2023-06-17 07:54:22,277] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:54:22,277] [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_018128325.1	s__Arachnia rubra	99.2061	879	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.26	99.21	0.97	0.97	4	conclusive
GCF_900637725.1	s__Arachnia propionica	82.1624	572	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.87	97.26	0.96	0.91	9	-
GCA_905372155.1	s__Arachnia sp905372155	82.0935	501	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900607225.1	s__Arachnia sp900607225	81.9789	553	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333945.2	s__Arachnia sp013333945	80.5279	442	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003859805.1	s__Arachnia propionica_C	78.9335	332	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932785.1	s__Arachnia propionica_B	78.8532	325	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197885.1	s__Arachnia rhinocerotis	77.8773	206	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998865.1	s__Arachnia flavescens	77.6834	200	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714275.1	s__Arachnia sp016714275	77.4656	188	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514785.1	s__Arachnia sp012514785	76.7859	102	906	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 07:54:22,280] [INFO] GTDB search result was written to GCA_013333735.2_ASM1333373v2_genomic.fna/result_gtdb.tsv
[2023-06-17 07:54:22,280] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:54:22,284] [INFO] DFAST_QC result json was written to GCA_013333735.2_ASM1333373v2_genomic.fna/dqc_result.json
[2023-06-17 07:54:22,284] [INFO] DFAST_QC completed!
[2023-06-17 07:54:22,285] [INFO] Total running time: 0h0m59s