[2023-06-19 06:45:25,770] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:45:25,772] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:45:25,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference
[2023-06-19 06:45:27,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:45:27,091] [INFO] Task started: Prodigal
[2023-06-19 06:45:27,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg97b5e982-db9e-4cea-aa9c-3264799f0390/GCA_018375595.1_ASM1837559v1_genomic.fna.gz | prodigal -d GCA_018375595.1_ASM1837559v1_genomic.fna/cds.fna -a GCA_018375595.1_ASM1837559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:45:34,995] [INFO] Task succeeded: Prodigal
[2023-06-19 06:45:34,996] [INFO] Task started: HMMsearch
[2023-06-19 06:45:34,996] [INFO] Running command: hmmsearch --tblout GCA_018375595.1_ASM1837559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/reference_markers.hmm GCA_018375595.1_ASM1837559v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:45:35,252] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:45:35,254] [INFO] Found 6/6 markers.
[2023-06-19 06:45:35,294] [INFO] Query marker FASTA was written to GCA_018375595.1_ASM1837559v1_genomic.fna/markers.fasta
[2023-06-19 06:45:35,295] [INFO] Task started: Blastn
[2023-06-19 06:45:35,295] [INFO] Running command: blastn -query GCA_018375595.1_ASM1837559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/reference_markers.fasta -out GCA_018375595.1_ASM1837559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:45:36,323] [INFO] Task succeeded: Blastn
[2023-06-19 06:45:36,326] [INFO] Selected 13 target genomes.
[2023-06-19 06:45:36,327] [INFO] Target genome list was writen to GCA_018375595.1_ASM1837559v1_genomic.fna/target_genomes.txt
[2023-06-19 06:45:36,331] [INFO] Task started: fastANI
[2023-06-19 06:45:36,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b5e982-db9e-4cea-aa9c-3264799f0390/GCA_018375595.1_ASM1837559v1_genomic.fna.gz --refList GCA_018375595.1_ASM1837559v1_genomic.fna/target_genomes.txt --output GCA_018375595.1_ASM1837559v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:45:43,481] [INFO] Task succeeded: fastANI
[2023-06-19 06:45:43,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:45:43,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:45:43,496] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 06:45:43,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 06:45:43,497] [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
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	96.2987	714	814	95	conclusive
Cutibacterium acnes subsp. defendens	strain=ATCC 11828	GCA_000231215.1	1905725	1747	type	True	81.797	531	814	95	below_threshold
Cutibacterium acnes	strain=DSM 1897	GCA_000472405.1	1747	1747	type	True	81.6982	532	814	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_003030305.1	1747	1747	type	True	81.6728	537	814	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_008728435.1	1747	1747	type	True	81.6489	538	814	95	below_threshold
Cutibacterium acnes	strain=ATCC 6919	GCA_000730485.1	1747	1747	type	True	81.6159	514	814	95	below_threshold
Cutibacterium namnetense	strain=NTS 31307302	GCA_001642025.1	1574624	1574624	type	True	81.5509	509	814	95	below_threshold
Cutibacterium modestum	strain=M12	GCA_008326345.1	2559073	2559073	type	True	81.3808	530	814	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.0835	142	814	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	77.0087	90	814	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.8345	97	814	95	below_threshold
Nocardioides alcanivorans	strain=NGK65	GCA_021555175.1	2897352	2897352	type	True	76.7488	86	814	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	76.6809	90	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:45:43,499] [INFO] DFAST Taxonomy check result was written to GCA_018375595.1_ASM1837559v1_genomic.fna/tc_result.tsv
[2023-06-19 06:45:43,500] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:45:43,500] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:45:43,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/checkm_data
[2023-06-19 06:45:43,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:45:43,536] [INFO] Task started: CheckM
[2023-06-19 06:45:43,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018375595.1_ASM1837559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018375595.1_ASM1837559v1_genomic.fna/checkm_input GCA_018375595.1_ASM1837559v1_genomic.fna/checkm_result
[2023-06-19 06:46:14,137] [INFO] Task succeeded: CheckM
[2023-06-19 06:46:14,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:46:14,163] [INFO] ===== Completeness check finished =====
[2023-06-19 06:46:14,163] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:46:14,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018375595.1_ASM1837559v1_genomic.fna/markers.fasta)
[2023-06-19 06:46:14,164] [INFO] Task started: Blastn
[2023-06-19 06:46:14,164] [INFO] Running command: blastn -query GCA_018375595.1_ASM1837559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3789f74c-ebb4-4db4-9dd8-97d3c113eb06/dqc_reference/reference_markers_gtdb.fasta -out GCA_018375595.1_ASM1837559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:46:15,524] [INFO] Task succeeded: Blastn
[2023-06-19 06:46:15,528] [INFO] Selected 9 target genomes.
[2023-06-19 06:46:15,528] [INFO] Target genome list was writen to GCA_018375595.1_ASM1837559v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:46:15,535] [INFO] Task started: fastANI
[2023-06-19 06:46:15,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b5e982-db9e-4cea-aa9c-3264799f0390/GCA_018375595.1_ASM1837559v1_genomic.fna.gz --refList GCA_018375595.1_ASM1837559v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018375595.1_ASM1837559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:46:20,644] [INFO] Task succeeded: fastANI
[2023-06-19 06:46:20,661] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:46:20,661] [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_000227295.1	s__Cutibacterium avidum	96.2987	714	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	97.99	95.78	0.94	0.87	29	conclusive
GCF_003030305.1	s__Cutibacterium acnes	81.6728	537	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.06	96.60	0.98	0.92	326	-
GCF_001642025.1	s__Cutibacterium namnetense	81.551	509	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.52	99.43	0.97	0.94	5	-
GCF_008326345.1	s__Cutibacterium modestum	81.3808	530	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	99.93	99.74	1.00	0.99	9	-
GCF_009696315.1	s__Cutibacterium porci	80.6234	484	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900605005.1	s__Cutibacterium timonense	79.9924	365	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325455.1	s__Acidipropionibacterium virtanenii	79.2942	306	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.2042	116	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.1591	132	814	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:46:20,664] [INFO] GTDB search result was written to GCA_018375595.1_ASM1837559v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:46:20,664] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:46:20,697] [INFO] DFAST_QC result json was written to GCA_018375595.1_ASM1837559v1_genomic.fna/dqc_result.json
[2023-06-19 06:46:20,697] [INFO] DFAST_QC completed!
[2023-06-19 06:46:20,697] [INFO] Total running time: 0h0m55s