[2024-01-24 11:43:50,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:50,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:50,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference
[2024-01-24 11:43:51,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:51,970] [INFO] Task started: Prodigal
[2024-01-24 11:43:51,970] [INFO] Running command: gunzip -c /var/lib/cwl/stga9947ab7-c112-4fa6-8ab5-321ec3cb5e70/GCF_016110345.1_ASM1611034v1_genomic.fna.gz | prodigal -d GCF_016110345.1_ASM1611034v1_genomic.fna/cds.fna -a GCF_016110345.1_ASM1611034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:59,116] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:59,117] [INFO] Task started: HMMsearch
[2024-01-24 11:43:59,117] [INFO] Running command: hmmsearch --tblout GCF_016110345.1_ASM1611034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/reference_markers.hmm GCF_016110345.1_ASM1611034v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:59,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:59,308] [INFO] Found 6/6 markers.
[2024-01-24 11:43:59,330] [INFO] Query marker FASTA was written to GCF_016110345.1_ASM1611034v1_genomic.fna/markers.fasta
[2024-01-24 11:43:59,330] [INFO] Task started: Blastn
[2024-01-24 11:43:59,330] [INFO] Running command: blastn -query GCF_016110345.1_ASM1611034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/reference_markers.fasta -out GCF_016110345.1_ASM1611034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:59,976] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:59,979] [INFO] Selected 27 target genomes.
[2024-01-24 11:43:59,979] [INFO] Target genome list was writen to GCF_016110345.1_ASM1611034v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:00,092] [INFO] Task started: fastANI
[2024-01-24 11:44:00,092] [INFO] Running command: fastANI --query /var/lib/cwl/stga9947ab7-c112-4fa6-8ab5-321ec3cb5e70/GCF_016110345.1_ASM1611034v1_genomic.fna.gz --refList GCF_016110345.1_ASM1611034v1_genomic.fna/target_genomes.txt --output GCF_016110345.1_ASM1611034v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,287] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,299] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:16,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:16,300] [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
Fluviibacter phosphoraccumulans	strain=SHINM1	GCA_016110345.1	1751046	1751046	type	True	100.0	767	768	95	conclusive
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	78.1735	58	768	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	77.8995	55	768	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.7455	91	768	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.6519	100	768	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.6202	96	768	95	below_threshold
Pandoraea norimbergensis	strain=DSM 11628	GCA_001465545.3	93219	93219	type	True	77.5014	67	768	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.0798	79	768	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	76.7334	94	768	95	below_threshold
Cupriavidus basilensis	strain=DSM 11853	GCA_008801925.2	68895	68895	suspected-type	True	76.6963	74	768	95	below_threshold
Pandoraea iniqua	strain=LMG 31009	GCA_902459685.1	2508288	2508288	type	True	76.671	54	768	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.6663	85	768	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.382	64	768	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.2252	52	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,301] [INFO] DFAST Taxonomy check result was written to GCF_016110345.1_ASM1611034v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/checkm_data
[2024-01-24 11:44:16,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,326] [INFO] Task started: CheckM
[2024-01-24 11:44:16,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016110345.1_ASM1611034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016110345.1_ASM1611034v1_genomic.fna/checkm_input GCF_016110345.1_ASM1611034v1_genomic.fna/checkm_result
[2024-01-24 11:44:41,657] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:41,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,675] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:41,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:41,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016110345.1_ASM1611034v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:41,675] [INFO] Task started: Blastn
[2024-01-24 11:44:41,676] [INFO] Running command: blastn -query GCF_016110345.1_ASM1611034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05662214-5249-4e1a-9307-97deba372a08/dqc_reference/reference_markers_gtdb.fasta -out GCF_016110345.1_ASM1611034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:42,639] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:42,642] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:42,643] [INFO] Target genome list was writen to GCF_016110345.1_ASM1611034v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:42,655] [INFO] Task started: fastANI
[2024-01-24 11:44:42,655] [INFO] Running command: fastANI --query /var/lib/cwl/stga9947ab7-c112-4fa6-8ab5-321ec3cb5e70/GCF_016110345.1_ASM1611034v1_genomic.fna.gz --refList GCF_016110345.1_ASM1611034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016110345.1_ASM1611034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:51,782] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:51,791] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:51,791] [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_016110345.1	s__Fluviibacter phosphoraccumulans	100.0	765	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.06	98.97	0.90	0.90	3	conclusive
GCA_903870055.1	s__Fluviibacter sp903870055	84.4863	413	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	99.89	99.89	0.98	0.98	2	-
GCA_018883265.1	s__Fluviibacter sp018883265	79.7738	256	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883385.1	s__Fluviibacter sp018883385	79.1689	214	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fluviibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864195.1	s__Azonexus sp016864195	78.0776	102	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	77.8874	83	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	77.8146	85	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379165.1	s__Azonexus sp004379165	77.2308	89	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.95	0.95	2	-
GCA_008080565.1	s__Azonexus sp008080565	76.9864	83	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391255.1	s__Azonexus sp011391255	76.9742	78	768	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,793] [INFO] GTDB search result was written to GCF_016110345.1_ASM1611034v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:51,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:51,796] [INFO] DFAST_QC result json was written to GCF_016110345.1_ASM1611034v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:51,797] [INFO] DFAST_QC completed!
[2024-01-24 11:44:51,797] [INFO] Total running time: 0h1m1s