[2024-01-25 19:43:35,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:35,397] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:35,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference
[2024-01-25 19:43:36,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:36,540] [INFO] Task started: Prodigal
[2024-01-25 19:43:36,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f43b96b-26f9-4cf4-a941-ae757a47dbe7/GCF_014203155.1_ASM1420315v1_genomic.fna.gz | prodigal -d GCF_014203155.1_ASM1420315v1_genomic.fna/cds.fna -a GCF_014203155.1_ASM1420315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:48,830] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:48,830] [INFO] Task started: HMMsearch
[2024-01-25 19:43:48,831] [INFO] Running command: hmmsearch --tblout GCF_014203155.1_ASM1420315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/reference_markers.hmm GCF_014203155.1_ASM1420315v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:49,123] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:49,124] [INFO] Found 6/6 markers.
[2024-01-25 19:43:49,163] [INFO] Query marker FASTA was written to GCF_014203155.1_ASM1420315v1_genomic.fna/markers.fasta
[2024-01-25 19:43:49,164] [INFO] Task started: Blastn
[2024-01-25 19:43:49,164] [INFO] Running command: blastn -query GCF_014203155.1_ASM1420315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/reference_markers.fasta -out GCF_014203155.1_ASM1420315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:50,232] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:50,236] [INFO] Selected 8 target genomes.
[2024-01-25 19:43:50,237] [INFO] Target genome list was writen to GCF_014203155.1_ASM1420315v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:50,238] [INFO] Task started: fastANI
[2024-01-25 19:43:50,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f43b96b-26f9-4cf4-a941-ae757a47dbe7/GCF_014203155.1_ASM1420315v1_genomic.fna.gz --refList GCF_014203155.1_ASM1420315v1_genomic.fna/target_genomes.txt --output GCF_014203155.1_ASM1420315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:02,766] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:02,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:02,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:02,773] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:02,773] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:02,773] [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
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	100.0	1597	1599	95	conclusive
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	88.4083	1071	1599	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	88.3846	1076	1599	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	88.1667	1222	1599	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	88.0191	1209	1599	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	86.4228	1042	1599	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	86.055	1184	1599	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	85.9549	1065	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:02,774] [INFO] DFAST Taxonomy check result was written to GCF_014203155.1_ASM1420315v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:02,775] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:02,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:02,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/checkm_data
[2024-01-25 19:44:02,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:02,830] [INFO] Task started: CheckM
[2024-01-25 19:44:02,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203155.1_ASM1420315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203155.1_ASM1420315v1_genomic.fna/checkm_input GCF_014203155.1_ASM1420315v1_genomic.fna/checkm_result
[2024-01-25 19:44:40,268] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:40,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:40,284] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:40,285] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:40,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203155.1_ASM1420315v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:40,285] [INFO] Task started: Blastn
[2024-01-25 19:44:40,285] [INFO] Running command: blastn -query GCF_014203155.1_ASM1420315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg451ffc7c-0c8c-4ee7-af54-da5ac4b04738/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203155.1_ASM1420315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:42,456] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:42,458] [INFO] Selected 8 target genomes.
[2024-01-25 19:44:42,458] [INFO] Target genome list was writen to GCF_014203155.1_ASM1420315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:42,466] [INFO] Task started: fastANI
[2024-01-25 19:44:42,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f43b96b-26f9-4cf4-a941-ae757a47dbe7/GCF_014203155.1_ASM1420315v1_genomic.fna.gz --refList GCF_014203155.1_ASM1420315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203155.1_ASM1420315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:53,264] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:53,270] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:53,270] [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_014203155.1	s__Shinella fusca	100.0	1597	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003574625.1	s__Shinella zoogloeoides_A	88.6647	1171	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	88.5708	1178	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	88.4127	1070	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	88.0363	1207	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_001262505.1	s__Shinella sp001262505	86.5614	1218	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_003432075.1	s__Shinella sp003432075	86.2036	1142	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	77.4834	159	1599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:53,272] [INFO] GTDB search result was written to GCF_014203155.1_ASM1420315v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:53,273] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:53,275] [INFO] DFAST_QC result json was written to GCF_014203155.1_ASM1420315v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:53,275] [INFO] DFAST_QC completed!
[2024-01-25 19:44:53,275] [INFO] Total running time: 0h1m18s