[2024-01-24 13:25:58,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,048] [INFO] DQC Reference Directory: /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,376] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b14038a-5335-4611-83b9-4f40c4755c78/GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/cds.fna -a GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:05,597] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:05,598] [INFO] Task started: HMMsearch
[2024-01-24 13:26:05,598] [INFO] Running command: hmmsearch --tblout GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/reference_markers.hmm GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:05,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:05,857] [INFO] Found 6/6 markers.
[2024-01-24 13:26:05,882] [INFO] Query marker FASTA was written to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:26:05,883] [INFO] Task started: Blastn
[2024-01-24 13:26:05,883] [INFO] Running command: blastn -query GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/reference_markers.fasta -out GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:06,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:06,484] [INFO] Selected 26 target genomes.
[2024-01-24 13:26:06,485] [INFO] Target genome list was writen to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:26:06,498] [INFO] Task started: fastANI
[2024-01-24 13:26:06,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b14038a-5335-4611-83b9-4f40c4755c78/GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna.gz --refList GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:19,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:19,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:19,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:19,302] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:19,302] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:19,302] [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
Pisciglobus halotolerans	strain=DSM 27630	GCA_900113675.1	745365	745365	type	True	100.0	767	769	95	conclusive
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000407505.1	154621	154621	type	True	78.6333	54	769	95	below_threshold
Enterococcus phoeniculicola	strain=ATCC BAA-412	GCA_000394035.1	154621	154621	type	True	78.5555	55	769	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	77.6752	100	769	95	below_threshold
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	77.5069	52	769	95	below_threshold
Carnobacterium iners	strain=LMG26642	GCA_900177385.1	1073423	1073423	type	True	77.3214	70	769	95	below_threshold
Carnobacterium iners	strain=DSM 28070	GCA_900109585.1	1073423	1073423	type	True	77.2471	71	769	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	77.2019	97	769	95	below_threshold
Carnobacterium alterfunditum	strain=pf4	GCA_000744115.1	28230	28230	type	True	76.9507	84	769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:19,304] [INFO] DFAST Taxonomy check result was written to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:19,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:19,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:19,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/checkm_data
[2024-01-24 13:26:19,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:19,336] [INFO] Task started: CheckM
[2024-01-24 13:26:19,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/checkm_input GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:26:42,784] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:42,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:42,805] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:42,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:42,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:26:42,807] [INFO] Task started: Blastn
[2024-01-24 13:26:42,807] [INFO] Running command: blastn -query GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd36dc251-0a43-45f0-9631-f2a2ff72523f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:43,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:43,720] [INFO] Selected 25 target genomes.
[2024-01-24 13:26:43,720] [INFO] Target genome list was writen to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:43,747] [INFO] Task started: fastANI
[2024-01-24 13:26:43,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b14038a-5335-4611-83b9-4f40c4755c78/GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna.gz --refList GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:57,558] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:57,571] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:57,572] [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_900113675.1	s__Pisciglobus halotolerans	100.0	767	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Pisciglobus	95.0	98.56	98.56	0.92	0.92	2	conclusive
GCF_000407505.1	s__Enterococcus_B phoeniculicola	78.6671	53	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.99	99.99	1.00	1.00	3	-
GCF_016892605.1	s__Desemzia sp016892605	78.2056	130	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Desemzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744375.1	s__Carnobacterium gallinarum	77.479	54	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483965.1	s__Carnobacterium_A sp001483965	77.3277	93	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.95	98.95	0.90	0.90	2	-
GCF_900177385.1	s__Carnobacterium_A iners	77.3276	69	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000746825.1	s__Carnobacterium_A inhibens	77.2303	98	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.16	98.07	0.90	0.88	3	-
GCF_002148425.1	s__Enterococcus sp002148425	76.9863	53	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
GCF_000744115.1	s__Carnobacterium_A alterfunditum	76.9507	84	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.24	96.49	0.94	0.89	3	-
GCF_002140175.1	s__Enterococcus_B sp002140175	76.5888	57	769	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_B	95.0	99.33	99.33	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:57,573] [INFO] GTDB search result was written to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:57,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:57,579] [INFO] DFAST_QC result json was written to GCF_900113675.1_IMG-taxon_2634166901_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:26:57,580] [INFO] DFAST_QC completed!
[2024-01-24 13:26:57,580] [INFO] Total running time: 0h0m60s