[2024-01-24 12:47:12,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,405] [INFO] DQC Reference Directory: /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference
[2024-01-24 12:47:13,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,848] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dc3f071-a3b6-42c8-b48c-763b71337642/GCF_009497155.1_ASM949715v1_genomic.fna.gz | prodigal -d GCF_009497155.1_ASM949715v1_genomic.fna/cds.fna -a GCF_009497155.1_ASM949715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:26,610] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:26,611] [INFO] Task started: HMMsearch
[2024-01-24 12:47:26,611] [INFO] Running command: hmmsearch --tblout GCF_009497155.1_ASM949715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/reference_markers.hmm GCF_009497155.1_ASM949715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:26,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:26,890] [INFO] Found 6/6 markers.
[2024-01-24 12:47:26,930] [INFO] Query marker FASTA was written to GCF_009497155.1_ASM949715v1_genomic.fna/markers.fasta
[2024-01-24 12:47:26,931] [INFO] Task started: Blastn
[2024-01-24 12:47:26,931] [INFO] Running command: blastn -query GCF_009497155.1_ASM949715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/reference_markers.fasta -out GCF_009497155.1_ASM949715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:27,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:27,702] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:27,702] [INFO] Target genome list was writen to GCF_009497155.1_ASM949715v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:27,709] [INFO] Task started: fastANI
[2024-01-24 12:47:27,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dc3f071-a3b6-42c8-b48c-763b71337642/GCF_009497155.1_ASM949715v1_genomic.fna.gz --refList GCF_009497155.1_ASM949715v1_genomic.fna/target_genomes.txt --output GCF_009497155.1_ASM949715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:40,641] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:40,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:40,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:40,655] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:40,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:40,655] [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 soli	strain=GS1	GCA_009497155.1	2590999	2590999	type	True	100.0	1406	1406	95	conclusive
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	78.4044	335	1406	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.079	283	1406	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	77.9516	293	1406	95	below_threshold
Glaciimonas immobilis	strain=DSM 23240	GCA_011947285.1	728004	728004	type	True	77.9066	227	1406	95	below_threshold
Glaciimonas immobilis	strain=DSM 23240	GCA_014202815.1	728004	728004	type	True	77.8763	223	1406	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	77.5764	123	1406	95	below_threshold
Solimicrobium silvestre	strain=S20-91	GCA_002976435.1	2099400	2099400	type	True	77.3381	136	1406	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	77.3083	125	1406	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	77.2363	98	1406	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	77.0967	131	1406	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.6396	70	1406	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	76.4333	73	1406	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.2683	95	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:40,657] [INFO] DFAST Taxonomy check result was written to GCF_009497155.1_ASM949715v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:40,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:40,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:40,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/checkm_data
[2024-01-24 12:47:40,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:40,701] [INFO] Task started: CheckM
[2024-01-24 12:47:40,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009497155.1_ASM949715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009497155.1_ASM949715v1_genomic.fna/checkm_input GCF_009497155.1_ASM949715v1_genomic.fna/checkm_result
[2024-01-24 12:48:23,509] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:23,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:23,539] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:23,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:23,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009497155.1_ASM949715v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:23,540] [INFO] Task started: Blastn
[2024-01-24 12:48:23,540] [INFO] Running command: blastn -query GCF_009497155.1_ASM949715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33b1ca2-61b9-4478-8105-8d2b4147ed03/dqc_reference/reference_markers_gtdb.fasta -out GCF_009497155.1_ASM949715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:24,696] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:24,699] [INFO] Selected 23 target genomes.
[2024-01-24 12:48:24,699] [INFO] Target genome list was writen to GCF_009497155.1_ASM949715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:24,714] [INFO] Task started: fastANI
[2024-01-24 12:48:24,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dc3f071-a3b6-42c8-b48c-763b71337642/GCF_009497155.1_ASM949715v1_genomic.fna.gz --refList GCF_009497155.1_ASM949715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009497155.1_ASM949715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:41,690] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:41,712] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:41,712] [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_009497155.1	s__Glaciimonas soli	100.0	1406	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107095.1	s__Collimonas sp900107095	78.4776	337	1406	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	78.473	363	1406	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	78.4089	333	1406	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	78.3587	336	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056055.1	s__Glaciimonas sp003056055	78.1971	319	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	78.1706	268	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_001584185.1	s__Collimonas pratensis	78.1563	293	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_000786695.1	s__Collimonas arenae_A	78.1508	296	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584145.1	s__Collimonas fungivorans	78.0543	283	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016917355.1	s__Glaciimonas sp016917355	78.0149	255	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	78.0026	275	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCF_001584165.1	s__Collimonas arenae	77.9184	294	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	99.97	99.97	1.00	1.00	2	-
GCF_011947285.1	s__Glaciimonas immobilis	77.8988	227	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002325825.1	s__Collimonas sp002325825	77.6689	99	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284115.1	s__Undibacterium sp014284115	77.6456	93	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201815.1	s__Undibacterium pigrum	77.5451	123	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464355.1	s__Herminiimonas sp001464355	77.401	155	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	77.2941	125	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377145.1	s__Glaciimonas sp014377145	76.8393	105	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Glaciimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770855.1	s__MESE01 sp001770855	76.7852	104	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MESE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	76.6357	133	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377155.1	s__CAILRJ01 sp014377155	76.2019	97	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:41,714] [INFO] GTDB search result was written to GCF_009497155.1_ASM949715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:41,715] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:41,720] [INFO] DFAST_QC result json was written to GCF_009497155.1_ASM949715v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:41,720] [INFO] DFAST_QC completed!
[2024-01-24 12:48:41,720] [INFO] Total running time: 0h1m29s