[2024-01-25 18:05:50,436] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:50,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:50,438] [INFO] DQC Reference Directory: /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference
[2024-01-25 18:05:51,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:51,567] [INFO] Task started: Prodigal
[2024-01-25 18:05:51,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg096a0c73-e5a2-4ab1-8569-453596d98d73/GCF_018304945.1_ASM1830494v1_genomic.fna.gz | prodigal -d GCF_018304945.1_ASM1830494v1_genomic.fna/cds.fna -a GCF_018304945.1_ASM1830494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:10,464] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:10,465] [INFO] Task started: HMMsearch
[2024-01-25 18:06:10,465] [INFO] Running command: hmmsearch --tblout GCF_018304945.1_ASM1830494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/reference_markers.hmm GCF_018304945.1_ASM1830494v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:10,722] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:10,723] [INFO] Found 6/6 markers.
[2024-01-25 18:06:10,765] [INFO] Query marker FASTA was written to GCF_018304945.1_ASM1830494v1_genomic.fna/markers.fasta
[2024-01-25 18:06:10,766] [INFO] Task started: Blastn
[2024-01-25 18:06:10,766] [INFO] Running command: blastn -query GCF_018304945.1_ASM1830494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/reference_markers.fasta -out GCF_018304945.1_ASM1830494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:11,721] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:11,724] [INFO] Selected 11 target genomes.
[2024-01-25 18:06:11,724] [INFO] Target genome list was writen to GCF_018304945.1_ASM1830494v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:11,730] [INFO] Task started: fastANI
[2024-01-25 18:06:11,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg096a0c73-e5a2-4ab1-8569-453596d98d73/GCF_018304945.1_ASM1830494v1_genomic.fna.gz --refList GCF_018304945.1_ASM1830494v1_genomic.fna/target_genomes.txt --output GCF_018304945.1_ASM1830494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:24,626] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:24,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:24,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:24,635] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:24,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:24,635] [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
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	100.0	1862	1863	95	conclusive
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	90.152	1407	1863	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	86.3011	1233	1863	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	84.8669	1125	1863	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	84.2096	1075	1863	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	83.768	1098	1863	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	80.5275	584	1863	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.2981	462	1863	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.1234	417	1863	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	78.7871	500	1863	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	78.7243	581	1863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:24,640] [INFO] DFAST Taxonomy check result was written to GCF_018304945.1_ASM1830494v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:24,641] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:24,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:24,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/checkm_data
[2024-01-25 18:06:24,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:24,697] [INFO] Task started: CheckM
[2024-01-25 18:06:24,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018304945.1_ASM1830494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018304945.1_ASM1830494v1_genomic.fna/checkm_input GCF_018304945.1_ASM1830494v1_genomic.fna/checkm_result
[2024-01-25 18:07:18,772] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:18,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:18,797] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:18,798] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:18,799] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018304945.1_ASM1830494v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:18,799] [INFO] Task started: Blastn
[2024-01-25 18:07:18,799] [INFO] Running command: blastn -query GCF_018304945.1_ASM1830494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga609114c-5a0a-4b5e-818b-11250dfe7db3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018304945.1_ASM1830494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:20,773] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:20,777] [INFO] Selected 8 target genomes.
[2024-01-25 18:07:20,778] [INFO] Target genome list was writen to GCF_018304945.1_ASM1830494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:20,789] [INFO] Task started: fastANI
[2024-01-25 18:07:20,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg096a0c73-e5a2-4ab1-8569-453596d98d73/GCF_018304945.1_ASM1830494v1_genomic.fna.gz --refList GCF_018304945.1_ASM1830494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018304945.1_ASM1830494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:32,510] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:32,516] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:32,516] [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_018304945.1	s__Collimonas sp018304945	100.0	1862	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	conclusive
GCF_002564105.1	s__Collimonas sp002564105	93.4798	1533	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	90.1486	1407	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_000221045.1	s__Collimonas fungivorans_A	86.3726	1219	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_001584145.1	s__Collimonas fungivorans	86.3216	1230	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	86.2661	1264	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_000786695.1	s__Collimonas arenae_A	85.4795	1345	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584165.1	s__Collimonas arenae	83.7549	1100	1863	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:32,518] [INFO] GTDB search result was written to GCF_018304945.1_ASM1830494v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:32,519] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:32,521] [INFO] DFAST_QC result json was written to GCF_018304945.1_ASM1830494v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:32,521] [INFO] DFAST_QC completed!
[2024-01-25 18:07:32,521] [INFO] Total running time: 0h1m42s