[2024-01-24 13:50:10,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference
[2024-01-24 13:50:11,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,601] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg206982cf-0caf-4693-bcde-d952cd1644cb/GCF_014699135.1_ASM1469913v1_genomic.fna.gz | prodigal -d GCF_014699135.1_ASM1469913v1_genomic.fna/cds.fna -a GCF_014699135.1_ASM1469913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:23,247] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:23,248] [INFO] Task started: HMMsearch
[2024-01-24 13:50:23,248] [INFO] Running command: hmmsearch --tblout GCF_014699135.1_ASM1469913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/reference_markers.hmm GCF_014699135.1_ASM1469913v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:23,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:23,547] [INFO] Found 6/6 markers.
[2024-01-24 13:50:23,580] [INFO] Query marker FASTA was written to GCF_014699135.1_ASM1469913v1_genomic.fna/markers.fasta
[2024-01-24 13:50:23,580] [INFO] Task started: Blastn
[2024-01-24 13:50:23,581] [INFO] Running command: blastn -query GCF_014699135.1_ASM1469913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/reference_markers.fasta -out GCF_014699135.1_ASM1469913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:24,302] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:24,305] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:24,305] [INFO] Target genome list was writen to GCF_014699135.1_ASM1469913v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:24,312] [INFO] Task started: fastANI
[2024-01-24 13:50:24,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg206982cf-0caf-4693-bcde-d952cd1644cb/GCF_014699135.1_ASM1469913v1_genomic.fna.gz --refList GCF_014699135.1_ASM1469913v1_genomic.fna/target_genomes.txt --output GCF_014699135.1_ASM1469913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:39,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:39,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:39,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:39,149] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:39,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:39,150] [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
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	100.0	1293	1293	95	conclusive
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	92.1356	1183	1293	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	79.6845	535	1293	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	79.1633	470	1293	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	79.1603	396	1293	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	79.102	460	1293	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	79.0224	442	1293	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.9044	419	1293	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.7082	405	1293	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	78.6121	421	1293	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	78.3688	195	1293	95	below_threshold
Sapientia aquatica	strain=SA-152	GCA_004358105.1	1549640	1549640	type	True	77.1111	140	1293	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	75.9886	88	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,151] [INFO] DFAST Taxonomy check result was written to GCF_014699135.1_ASM1469913v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:39,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:39,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:39,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/checkm_data
[2024-01-24 13:50:39,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:39,191] [INFO] Task started: CheckM
[2024-01-24 13:50:39,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014699135.1_ASM1469913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014699135.1_ASM1469913v1_genomic.fna/checkm_input GCF_014699135.1_ASM1469913v1_genomic.fna/checkm_result
[2024-01-24 13:51:15,003] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:15,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:15,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:15,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:15,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014699135.1_ASM1469913v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:15,024] [INFO] Task started: Blastn
[2024-01-24 13:51:15,024] [INFO] Running command: blastn -query GCF_014699135.1_ASM1469913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54ef5e30-cf2e-4f01-9f35-e4104db08247/dqc_reference/reference_markers_gtdb.fasta -out GCF_014699135.1_ASM1469913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:16,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:16,117] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:16,117] [INFO] Target genome list was writen to GCF_014699135.1_ASM1469913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:16,371] [INFO] Task started: fastANI
[2024-01-24 13:51:16,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg206982cf-0caf-4693-bcde-d952cd1644cb/GCF_014699135.1_ASM1469913v1_genomic.fna.gz --refList GCF_014699135.1_ASM1469913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014699135.1_ASM1469913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:29,410] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:29,426] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:29,426] [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_014699135.1	s__Undibacterium aquatile	100.0	1293	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	conclusive
GCF_018139565.1	s__Undibacterium sp018139565	92.1356	1183	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377855.1	s__Undibacterium oligocarboniphilum	79.6755	502	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014284195.1	s__Undibacterium sp014284195	79.6752	536	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284235.1	s__Undibacterium sp014284235	79.1745	468	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284255.1	s__Undibacterium jejuense	79.1648	396	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	79.104	459	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937975.1	s__Undibacterium sp009937975	79.0457	400	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284365.1	s__Undibacterium sp014284365	79.0136	442	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_009937955.1	s__Undibacterium sp009937955	78.9869	398	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201815.1	s__Undibacterium pigrum	78.7048	405	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200895.1	s__Undibacterium sp016200895	78.6198	374	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016196925.1	s__Undibacterium sp016196925	78.4217	332	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284305.1	s__Undibacterium seohonense	78.3688	195	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358105.1	s__Solimicrobium aquaticum	77.128	139	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:29,428] [INFO] GTDB search result was written to GCF_014699135.1_ASM1469913v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:29,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:29,433] [INFO] DFAST_QC result json was written to GCF_014699135.1_ASM1469913v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:29,433] [INFO] DFAST_QC completed!
[2024-01-24 13:51:29,433] [INFO] Total running time: 0h1m19s