[2024-01-24 14:19:34,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:34,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:34,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference
[2024-01-24 14:19:35,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:35,959] [INFO] Task started: Prodigal
[2024-01-24 14:19:35,960] [INFO] Running command: gunzip -c /var/lib/cwl/stgc15873b0-5020-4616-8fe1-0b1609c3dd23/GCF_003201475.1_ASM320147v1_genomic.fna.gz | prodigal -d GCF_003201475.1_ASM320147v1_genomic.fna/cds.fna -a GCF_003201475.1_ASM320147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:58,691] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:58,692] [INFO] Task started: HMMsearch
[2024-01-24 14:19:58,692] [INFO] Running command: hmmsearch --tblout GCF_003201475.1_ASM320147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/reference_markers.hmm GCF_003201475.1_ASM320147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:59,065] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:59,066] [INFO] Found 6/6 markers.
[2024-01-24 14:19:59,140] [INFO] Query marker FASTA was written to GCF_003201475.1_ASM320147v1_genomic.fna/markers.fasta
[2024-01-24 14:19:59,140] [INFO] Task started: Blastn
[2024-01-24 14:19:59,141] [INFO] Running command: blastn -query GCF_003201475.1_ASM320147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/reference_markers.fasta -out GCF_003201475.1_ASM320147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:00,197] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:00,200] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:00,200] [INFO] Target genome list was writen to GCF_003201475.1_ASM320147v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:00,228] [INFO] Task started: fastANI
[2024-01-24 14:20:00,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15873b0-5020-4616-8fe1-0b1609c3dd23/GCF_003201475.1_ASM320147v1_genomic.fna.gz --refList GCF_003201475.1_ASM320147v1_genomic.fna/target_genomes.txt --output GCF_003201475.1_ASM320147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:19,708] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:19,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:19,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:19,723] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:19,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:19,724] [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
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	100.0	2394	2397	95	conclusive
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_018398275.1	28210	28210	type	True	99.9949	2394	2397	95	conclusive
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.8874	576	2397	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	78.5259	481	2397	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	78.5226	482	2397	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	78.4968	450	2397	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	78.4008	446	2397	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	78.3801	442	2397	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	78.1006	434	2397	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.6764	398	2397	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.3217	387	2397	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	77.2159	299	2397	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.2135	455	2397	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.1614	354	2397	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.1475	446	2397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:19,726] [INFO] DFAST Taxonomy check result was written to GCF_003201475.1_ASM320147v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:19,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:19,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:19,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/checkm_data
[2024-01-24 14:20:19,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:19,799] [INFO] Task started: CheckM
[2024-01-24 14:20:19,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201475.1_ASM320147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201475.1_ASM320147v1_genomic.fna/checkm_input GCF_003201475.1_ASM320147v1_genomic.fna/checkm_result
[2024-01-24 14:21:23,673] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:23,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:23,694] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:23,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:23,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201475.1_ASM320147v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:23,695] [INFO] Task started: Blastn
[2024-01-24 14:21:23,695] [INFO] Running command: blastn -query GCF_003201475.1_ASM320147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0fddcd2-aafc-43a8-98f2-07028c3a1ccd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201475.1_ASM320147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:25,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:25,765] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:25,765] [INFO] Target genome list was writen to GCF_003201475.1_ASM320147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:25,825] [INFO] Task started: fastANI
[2024-01-24 14:21:25,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgc15873b0-5020-4616-8fe1-0b1609c3dd23/GCF_003201475.1_ASM320147v1_genomic.fna.gz --refList GCF_003201475.1_ASM320147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201475.1_ASM320147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:40,342] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:40,354] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:40,355] [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_003201475.1	s__Chelatococcus asaccharovorans	100.0	2394	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_018398335.1	s__Chelatococcus sp018398335	84.6626	1459	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398315.1	s__Chelatococcus sp018398315	83.4139	1314	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.9106	573	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	78.5095	483	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCF_014201415.1	s__Chelatococcus_A composti	78.401	446	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCA_900466745.1	s__Bosea sp900466745	78.1878	471	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_008253865.1	s__Bosea sp008253865	77.9669	478	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473415.1	s__Bosea sp900473415	77.711	454	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040035.1	s__Methylobacterium sp008040035	77.2673	270	2397	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:40,356] [INFO] GTDB search result was written to GCF_003201475.1_ASM320147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:40,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:40,360] [INFO] DFAST_QC result json was written to GCF_003201475.1_ASM320147v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:40,360] [INFO] DFAST_QC completed!
[2024-01-24 14:21:40,360] [INFO] Total running time: 0h2m6s