[2024-01-24 11:19:49,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:49,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:49,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference
[2024-01-24 11:19:50,215] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,216] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,216] [INFO] Running command: gunzip -c /var/lib/cwl/stg00c6286d-a161-4721-8645-f6a7580de1fc/GCF_018305005.1_ASM1830500v1_genomic.fna.gz | prodigal -d GCF_018305005.1_ASM1830500v1_genomic.fna/cds.fna -a GCF_018305005.1_ASM1830500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:08,849] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:08,850] [INFO] Task started: HMMsearch
[2024-01-24 11:20:08,850] [INFO] Running command: hmmsearch --tblout GCF_018305005.1_ASM1830500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/reference_markers.hmm GCF_018305005.1_ASM1830500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:09,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:09,147] [INFO] Found 6/6 markers.
[2024-01-24 11:20:09,202] [INFO] Query marker FASTA was written to GCF_018305005.1_ASM1830500v1_genomic.fna/markers.fasta
[2024-01-24 11:20:09,203] [INFO] Task started: Blastn
[2024-01-24 11:20:09,203] [INFO] Running command: blastn -query GCF_018305005.1_ASM1830500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/reference_markers.fasta -out GCF_018305005.1_ASM1830500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:10,131] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:10,135] [INFO] Selected 11 target genomes.
[2024-01-24 11:20:10,136] [INFO] Target genome list was writen to GCF_018305005.1_ASM1830500v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:10,143] [INFO] Task started: fastANI
[2024-01-24 11:20:10,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6286d-a161-4721-8645-f6a7580de1fc/GCF_018305005.1_ASM1830500v1_genomic.fna.gz --refList GCF_018305005.1_ASM1830500v1_genomic.fna/target_genomes.txt --output GCF_018305005.1_ASM1830500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:22,179] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:22,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:22,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:22,193] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:22,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:22,194] [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 silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	100.0	1760	1767	95	conclusive
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	87.0541	1065	1767	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	86.6725	1183	1767	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	84.8483	1138	1767	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	84.3492	1121	1767	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	83.3842	1005	1767	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.6739	472	1767	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	78.2576	402	1767	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	78.0751	344	1767	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	78.0233	320	1767	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	77.9979	404	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:22,196] [INFO] DFAST Taxonomy check result was written to GCF_018305005.1_ASM1830500v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:22,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:22,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:22,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/checkm_data
[2024-01-24 11:20:22,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:22,253] [INFO] Task started: CheckM
[2024-01-24 11:20:22,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018305005.1_ASM1830500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018305005.1_ASM1830500v1_genomic.fna/checkm_input GCF_018305005.1_ASM1830500v1_genomic.fna/checkm_result
[2024-01-24 11:21:16,540] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:16,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:16,572] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:16,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:16,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018305005.1_ASM1830500v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:16,574] [INFO] Task started: Blastn
[2024-01-24 11:21:16,574] [INFO] Running command: blastn -query GCF_018305005.1_ASM1830500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e99788c-595c-40d3-92b8-5e95617734a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_018305005.1_ASM1830500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:18,216] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:18,220] [INFO] Selected 9 target genomes.
[2024-01-24 11:21:18,221] [INFO] Target genome list was writen to GCF_018305005.1_ASM1830500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:18,241] [INFO] Task started: fastANI
[2024-01-24 11:21:18,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6286d-a161-4721-8645-f6a7580de1fc/GCF_018305005.1_ASM1830500v1_genomic.fna.gz --refList GCF_018305005.1_ASM1830500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018305005.1_ASM1830500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:29,299] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:29,311] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:29,312] [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_018305005.1	s__Collimonas sp018305005	100.0	1760	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107095.1	s__Collimonas sp900107095	87.8341	1209	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304965.1	s__Collimonas antrihumi	87.0662	1065	1767	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	86.9345	1240	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_000221045.1	s__Collimonas fungivorans_A	86.7719	1198	1767	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	86.6783	1182	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113705.1	s__Collimonas sp900113705	86.5526	1130	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111995.1	s__Collimonas sp900111995	86.4958	1131	1767	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	83.3868	1005	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:29,313] [INFO] GTDB search result was written to GCF_018305005.1_ASM1830500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:29,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:29,317] [INFO] DFAST_QC result json was written to GCF_018305005.1_ASM1830500v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:29,317] [INFO] DFAST_QC completed!
[2024-01-24 11:21:29,317] [INFO] Total running time: 0h1m40s