[2024-01-25 20:03:05,430] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference
[2024-01-25 20:03:06,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,542] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg7baa4367-5aed-43d1-b96c-073ab7a1dfd0/GCF_011947285.1_ASM1194728v1_genomic.fna.gz | prodigal -d GCF_011947285.1_ASM1194728v1_genomic.fna/cds.fna -a GCF_011947285.1_ASM1194728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:18,665] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:18,666] [INFO] Task started: HMMsearch
[2024-01-25 20:03:18,666] [INFO] Running command: hmmsearch --tblout GCF_011947285.1_ASM1194728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/reference_markers.hmm GCF_011947285.1_ASM1194728v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:18,950] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:18,951] [INFO] Found 6/6 markers.
[2024-01-25 20:03:18,989] [INFO] Query marker FASTA was written to GCF_011947285.1_ASM1194728v1_genomic.fna/markers.fasta
[2024-01-25 20:03:18,990] [INFO] Task started: Blastn
[2024-01-25 20:03:18,990] [INFO] Running command: blastn -query GCF_011947285.1_ASM1194728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/reference_markers.fasta -out GCF_011947285.1_ASM1194728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:19,672] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:19,675] [INFO] Selected 16 target genomes.
[2024-01-25 20:03:19,675] [INFO] Target genome list was writen to GCF_011947285.1_ASM1194728v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:19,688] [INFO] Task started: fastANI
[2024-01-25 20:03:19,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg7baa4367-5aed-43d1-b96c-073ab7a1dfd0/GCF_011947285.1_ASM1194728v1_genomic.fna.gz --refList GCF_011947285.1_ASM1194728v1_genomic.fna/target_genomes.txt --output GCF_011947285.1_ASM1194728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:34,390] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:34,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:34,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:34,402] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:34,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:34,402] [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
Glaciimonas immobilis	strain=DSM 23240	GCA_011947285.1	728004	728004	type	True	100.0	1621	1622	95	conclusive
Glaciimonas immobilis	strain=DSM 23240	GCA_014202815.1	728004	728004	type	True	99.9957	1614	1622	95	conclusive
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	77.9064	288	1622	95	below_threshold
Glaciimonas soli	strain=GS1	GCA_009497155.1	2590999	2590999	type	True	77.8968	231	1622	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	77.8213	263	1622	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	77.8094	268	1622	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.7157	267	1622	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.6919	262	1622	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	77.6642	291	1622	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.9176	106	1622	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	76.9124	101	1622	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.4652	72	1622	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	76.2609	102	1622	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.1069	95	1622	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	75.7435	62	1622	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	75.4634	50	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:34,406] [INFO] DFAST Taxonomy check result was written to GCF_011947285.1_ASM1194728v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:34,407] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:34,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:34,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/checkm_data
[2024-01-25 20:03:34,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:34,456] [INFO] Task started: CheckM
[2024-01-25 20:03:34,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011947285.1_ASM1194728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011947285.1_ASM1194728v1_genomic.fna/checkm_input GCF_011947285.1_ASM1194728v1_genomic.fna/checkm_result
[2024-01-25 20:04:12,576] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:12,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:12,597] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:12,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:12,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011947285.1_ASM1194728v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:12,598] [INFO] Task started: Blastn
[2024-01-25 20:04:12,598] [INFO] Running command: blastn -query GCF_011947285.1_ASM1194728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d6423d6-551b-4ace-9359-b8b4d8b867e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_011947285.1_ASM1194728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:13,733] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:13,735] [INFO] Selected 17 target genomes.
[2024-01-25 20:04:13,736] [INFO] Target genome list was writen to GCF_011947285.1_ASM1194728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:13,760] [INFO] Task started: fastANI
[2024-01-25 20:04:13,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg7baa4367-5aed-43d1-b96c-073ab7a1dfd0/GCF_011947285.1_ASM1194728v1_genomic.fna.gz --refList GCF_011947285.1_ASM1194728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011947285.1_ASM1194728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:30,803] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:30,814] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:30,814] [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_011947285.1	s__Glaciimonas immobilis	100.0	1621	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016917355.1	s__Glaciimonas sp016917355	79.4413	633	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056055.1	s__Glaciimonas sp003056055	79.0319	566	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786695.1	s__Collimonas arenae_A	78.1394	247	1622	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	77.9154	288	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497155.1	s__Glaciimonas soli	77.8951	230	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113705.1	s__Collimonas sp900113705	77.8658	287	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107095.1	s__Collimonas sp900107095	77.8547	271	1622	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	77.8381	284	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304945.1	s__Collimonas sp018304945	77.8219	263	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.22	98.22	0.87	0.87	2	-
GCF_001584165.1	s__Collimonas arenae	77.8094	268	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001584185.1	s__Collimonas pratensis	77.7157	267	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_001584145.1	s__Collimonas fungivorans	77.6917	262	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	77.6553	277	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_018305005.1	s__Collimonas sp018305005	77.6532	292	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377145.1	s__Glaciimonas sp014377145	77.6037	168	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857495.1	s__Duganella sp009857495	76.0345	101	1622	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	98.63	98.63	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:30,815] [INFO] GTDB search result was written to GCF_011947285.1_ASM1194728v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:30,816] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:30,819] [INFO] DFAST_QC result json was written to GCF_011947285.1_ASM1194728v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:30,819] [INFO] DFAST_QC completed!
[2024-01-25 20:04:30,819] [INFO] Total running time: 0h1m25s