[2024-01-24 15:11:11,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:11,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:11,071] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference
[2024-01-24 15:11:12,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:12,373] [INFO] Task started: Prodigal
[2024-01-24 15:11:12,373] [INFO] Running command: gunzip -c /var/lib/cwl/stge431bc8b-2e5f-405b-bba0-0e4025824179/GCF_003201595.1_ASM320159v1_genomic.fna.gz | prodigal -d GCF_003201595.1_ASM320159v1_genomic.fna/cds.fna -a GCF_003201595.1_ASM320159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:27,312] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:27,312] [INFO] Task started: HMMsearch
[2024-01-24 15:11:27,312] [INFO] Running command: hmmsearch --tblout GCF_003201595.1_ASM320159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/reference_markers.hmm GCF_003201595.1_ASM320159v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:27,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:27,656] [INFO] Found 6/6 markers.
[2024-01-24 15:11:27,704] [INFO] Query marker FASTA was written to GCF_003201595.1_ASM320159v1_genomic.fna/markers.fasta
[2024-01-24 15:11:27,705] [INFO] Task started: Blastn
[2024-01-24 15:11:27,705] [INFO] Running command: blastn -query GCF_003201595.1_ASM320159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/reference_markers.fasta -out GCF_003201595.1_ASM320159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:29,036] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:29,040] [INFO] Selected 16 target genomes.
[2024-01-24 15:11:29,041] [INFO] Target genome list was writen to GCF_003201595.1_ASM320159v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:29,048] [INFO] Task started: fastANI
[2024-01-24 15:11:29,048] [INFO] Running command: fastANI --query /var/lib/cwl/stge431bc8b-2e5f-405b-bba0-0e4025824179/GCF_003201595.1_ASM320159v1_genomic.fna.gz --refList GCF_003201595.1_ASM320159v1_genomic.fna/target_genomes.txt --output GCF_003201595.1_ASM320159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:46,814] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:46,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:46,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:46,832] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:46,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:46,833] [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
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	100.0	1451	1454	95	conclusive
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	83.5296	859	1454	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	83.4431	907	1454	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	83.3397	860	1454	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	82.8525	824	1454	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	82.7799	840	1454	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	81.1768	634	1454	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	81.1689	682	1454	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	81.0493	649	1454	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.9277	678	1454	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.9008	691	1454	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.7918	683	1454	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.6739	805	1454	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.4413	813	1454	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.9847	552	1454	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.7308	619	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:46,835] [INFO] DFAST Taxonomy check result was written to GCF_003201595.1_ASM320159v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:46,836] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:46,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:46,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/checkm_data
[2024-01-24 15:11:46,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:46,879] [INFO] Task started: CheckM
[2024-01-24 15:11:46,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201595.1_ASM320159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201595.1_ASM320159v1_genomic.fna/checkm_input GCF_003201595.1_ASM320159v1_genomic.fna/checkm_result
[2024-01-24 15:13:17,275] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:17,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:17,296] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:17,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:17,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201595.1_ASM320159v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:17,297] [INFO] Task started: Blastn
[2024-01-24 15:13:17,297] [INFO] Running command: blastn -query GCF_003201595.1_ASM320159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9395b18-cc5e-49f5-8be8-ce534346af4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201595.1_ASM320159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:19,630] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:19,635] [INFO] Selected 14 target genomes.
[2024-01-24 15:13:19,636] [INFO] Target genome list was writen to GCF_003201595.1_ASM320159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:19,672] [INFO] Task started: fastANI
[2024-01-24 15:13:19,673] [INFO] Running command: fastANI --query /var/lib/cwl/stge431bc8b-2e5f-405b-bba0-0e4025824179/GCF_003201595.1_ASM320159v1_genomic.fna.gz --refList GCF_003201595.1_ASM320159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201595.1_ASM320159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:36,624] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:36,642] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:36,642] [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_003201595.1	s__Sphaerotilus hippei	100.0	1451	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013294065.1	s__Sphaerotilus sp013294065	83.5257	927	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156335.1	s__Sphaerotilus natans	83.4693	904	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000019785.1	s__Leptothrix cholodnii	83.2227	887	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329925.1	s__Sphaerotilus sulfidivorans	83.2141	902	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013410775.1	s__Sphaerotilus montanus	82.7714	843	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004216565.1	s__Leptothrix mobilis	82.4533	815	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	81.2658	744	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	81.2221	770	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_000190375.1	s__Rubrivivax benzoatilyticus	80.9551	675	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.67	98.73	0.98	0.95	5	-
GCF_009760915.1	s__Azohydromonas aeria	80.7126	800	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	80.0483	657	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCA_005503085.1	s__Paucibacter_A sp005503085	79.8703	681	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467315.1	s__OAE585 sp016467315	79.4622	662	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__OAE585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:36,644] [INFO] GTDB search result was written to GCF_003201595.1_ASM320159v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:36,644] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:36,648] [INFO] DFAST_QC result json was written to GCF_003201595.1_ASM320159v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:36,648] [INFO] DFAST_QC completed!
[2024-01-24 15:13:36,648] [INFO] Total running time: 0h2m26s