[2024-01-24 14:28:07,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:07,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:07,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference
[2024-01-24 14:28:10,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,421] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ed74774-6e3d-4b5b-997e-b88f47f32dd5/GCF_018069865.1_ASM1806986v1_genomic.fna.gz | prodigal -d GCF_018069865.1_ASM1806986v1_genomic.fna/cds.fna -a GCF_018069865.1_ASM1806986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:32,252] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:32,252] [INFO] Task started: HMMsearch
[2024-01-24 14:28:32,252] [INFO] Running command: hmmsearch --tblout GCF_018069865.1_ASM1806986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/reference_markers.hmm GCF_018069865.1_ASM1806986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:32,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:32,571] [INFO] Found 6/6 markers.
[2024-01-24 14:28:32,623] [INFO] Query marker FASTA was written to GCF_018069865.1_ASM1806986v1_genomic.fna/markers.fasta
[2024-01-24 14:28:32,624] [INFO] Task started: Blastn
[2024-01-24 14:28:32,624] [INFO] Running command: blastn -query GCF_018069865.1_ASM1806986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/reference_markers.fasta -out GCF_018069865.1_ASM1806986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:33,588] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:33,591] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:33,592] [INFO] Target genome list was writen to GCF_018069865.1_ASM1806986v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:33,602] [INFO] Task started: fastANI
[2024-01-24 14:28:33,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed74774-6e3d-4b5b-997e-b88f47f32dd5/GCF_018069865.1_ASM1806986v1_genomic.fna.gz --refList GCF_018069865.1_ASM1806986v1_genomic.fna/target_genomes.txt --output GCF_018069865.1_ASM1806986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:48,678] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:48,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:48,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:48,694] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:48,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:48,694] [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
Ideonella paludis	strain=KCTC 32238	GCA_018069865.1	1233411	1233411	type	True	100.0	1589	1589	95	conclusive
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.8784	450	1589	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.7803	552	1589	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	79.7423	543	1589	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	79.7161	559	1589	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.5515	522	1589	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	78.8433	453	1589	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.7016	449	1589	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.6638	481	1589	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.6551	456	1589	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	78.5556	470	1589	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.5186	368	1589	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.4782	389	1589	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	78.0786	411	1589	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	77.959	419	1589	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	77.5209	269	1589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:48,696] [INFO] DFAST Taxonomy check result was written to GCF_018069865.1_ASM1806986v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:48,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:48,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:48,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/checkm_data
[2024-01-24 14:28:48,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:48,747] [INFO] Task started: CheckM
[2024-01-24 14:28:48,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018069865.1_ASM1806986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018069865.1_ASM1806986v1_genomic.fna/checkm_input GCF_018069865.1_ASM1806986v1_genomic.fna/checkm_result
[2024-01-24 14:30:04,924] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:04,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:04,948] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:04,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:04,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018069865.1_ASM1806986v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:04,949] [INFO] Task started: Blastn
[2024-01-24 14:30:04,949] [INFO] Running command: blastn -query GCF_018069865.1_ASM1806986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ad1465-1083-417b-bad9-18accea51414/dqc_reference/reference_markers_gtdb.fasta -out GCF_018069865.1_ASM1806986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:06,749] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:06,753] [INFO] Selected 14 target genomes.
[2024-01-24 14:30:06,754] [INFO] Target genome list was writen to GCF_018069865.1_ASM1806986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:07,177] [INFO] Task started: fastANI
[2024-01-24 14:30:07,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed74774-6e3d-4b5b-997e-b88f47f32dd5/GCF_018069865.1_ASM1806986v1_genomic.fna.gz --refList GCF_018069865.1_ASM1806986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018069865.1_ASM1806986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:21,752] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:21,767] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:21,767] [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_018069865.1	s__Ideonella paludis	100.0	1589	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004359425.1	s__Ideonella sp004359425	84.8475	1041	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	79.8375	663	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_018069755.1	s__Ideonella sp018069755	79.8218	693	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710065.1	s__Ideonella sp016710065	79.8074	635	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	99.07	99.00	0.95	0.93	3	-
GCA_002255925.1	s__Ideonella sp002255925	79.8041	614	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801845.1	s__Ideonella dechloratans	79.7614	541	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	79.6301	458	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	79.095	526	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780145.1	s__Ideonella sp018780145	78.974	560	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	78.6888	494	1589	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_004016505.1	s__Rubrivivax rivuli	78.3776	496	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	77.9878	449	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	77.9059	371	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:21,769] [INFO] GTDB search result was written to GCF_018069865.1_ASM1806986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:21,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:21,775] [INFO] DFAST_QC result json was written to GCF_018069865.1_ASM1806986v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:21,776] [INFO] DFAST_QC completed!
[2024-01-24 14:30:21,776] [INFO] Total running time: 0h2m14s