[2024-01-24 15:10:41,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,212] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference
[2024-01-24 15:10:42,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,635] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b7a56db-4a87-4789-878c-1158a1fb837c/GCF_000744375.1_ASM74437v1_genomic.fna.gz | prodigal -d GCF_000744375.1_ASM74437v1_genomic.fna/cds.fna -a GCF_000744375.1_ASM74437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,496] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,496] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,496] [INFO] Running command: hmmsearch --tblout GCF_000744375.1_ASM74437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/reference_markers.hmm GCF_000744375.1_ASM74437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:50,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:50,822] [INFO] Found 6/6 markers.
[2024-01-24 15:10:50,855] [INFO] Query marker FASTA was written to GCF_000744375.1_ASM74437v1_genomic.fna/markers.fasta
[2024-01-24 15:10:50,855] [INFO] Task started: Blastn
[2024-01-24 15:10:50,855] [INFO] Running command: blastn -query GCF_000744375.1_ASM74437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/reference_markers.fasta -out GCF_000744375.1_ASM74437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:51,508] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:51,512] [INFO] Selected 21 target genomes.
[2024-01-24 15:10:51,512] [INFO] Target genome list was writen to GCF_000744375.1_ASM74437v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:51,520] [INFO] Task started: fastANI
[2024-01-24 15:10:51,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b7a56db-4a87-4789-878c-1158a1fb837c/GCF_000744375.1_ASM74437v1_genomic.fna.gz --refList GCF_000744375.1_ASM74437v1_genomic.fna/target_genomes.txt --output GCF_000744375.1_ASM74437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:04,978] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:04,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:04,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:04,990] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:04,990] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:04,990] [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
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	100.0	1345	1345	95	conclusive
Carnobacterium maltaromaticum	strain=MX5	GCA_000744945.1	2751	2751	type	True	81.0596	530	1345	95	below_threshold
Carnobacterium maltaromaticum	strain=DSM 20342	GCA_001437315.1	2751	2751	type	True	80.4802	504	1345	95	below_threshold
Carnobacterium divergens	strain=NCTC13772	GCA_900446755.1	2748	2748	type	True	79.5946	309	1345	95	below_threshold
Carnobacterium viridans	strain=MPL-11	GCA_900102725.1	174587	174587	type	True	79.4644	137	1345	95	below_threshold
Carnobacterium inhibens subsp. gilichinskyi	strain=WN1359	GCA_000493735.1	1266845	147709	type	True	79.1696	153	1345	95	below_threshold
Carnobacterium jeotgali	strain=MS3	GCA_000745125.1	545534	545534	type	True	79.0587	137	1345	95	below_threshold
Carnobacterium divergens	strain=DSM 20623	GCA_001437085.1	2748	2748	type	True	79.0309	308	1345	95	below_threshold
Carnobacterium inhibens subsp. inhibens	strain=K1	GCA_000746825.1	1758721	147709	type	True	78.8708	143	1345	95	below_threshold
Carnobacterium mobile	strain=MT37L	GCA_000744825.1	2750	2750	type	True	78.7055	138	1345	95	below_threshold
Carnobacterium pleistocenium	strain=FTR1	GCA_000744285.1	181073	181073	type	True	78.3784	126	1345	95	below_threshold
Enterococcus ureilyticus	strain=CCUG 48799	GCA_002806915.1	1131292	1131292	type	True	77.2984	92	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:05,000] [INFO] DFAST Taxonomy check result was written to GCF_000744375.1_ASM74437v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:05,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:05,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:05,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/checkm_data
[2024-01-24 15:11:05,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:05,072] [INFO] Task started: CheckM
[2024-01-24 15:11:05,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744375.1_ASM74437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744375.1_ASM74437v1_genomic.fna/checkm_input GCF_000744375.1_ASM74437v1_genomic.fna/checkm_result
[2024-01-24 15:11:35,577] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:35,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:35,604] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:35,604] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:35,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744375.1_ASM74437v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:35,605] [INFO] Task started: Blastn
[2024-01-24 15:11:35,606] [INFO] Running command: blastn -query GCF_000744375.1_ASM74437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa96fc1f-ff63-40c4-825a-7bda0f5de483/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744375.1_ASM74437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:36,428] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:36,432] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:36,432] [INFO] Target genome list was writen to GCF_000744375.1_ASM74437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:36,446] [INFO] Task started: fastANI
[2024-01-24 15:11:36,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b7a56db-4a87-4789-878c-1158a1fb837c/GCF_000744375.1_ASM74437v1_genomic.fna.gz --refList GCF_000744375.1_ASM74437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744375.1_ASM74437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:45,952] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:45,969] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:45,970] [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_000744375.1	s__Carnobacterium gallinarum	100.0	1345	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744945.1	s__Carnobacterium maltaromaticum	81.1064	533	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	98.15	96.42	0.90	0.81	35	-
GCF_000744255.1	s__Carnobacterium divergens	79.5226	318	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.06	98.93	0.92	0.90	24	-
GCF_900258435.1	s__Carnobacterium divergens_A	79.3823	313	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium	95.0	99.21	98.87	0.95	0.92	17	-
GCF_900102725.1	s__Carnobacterium_A viridans	79.2474	138	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.44	98.44	0.88	0.88	2	-
GCF_000745125.1	s__Carnobacterium_A jeotgali	79.1455	137	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	99.33	98.67	0.94	0.87	3	-
GCF_000746825.1	s__Carnobacterium_A inhibens	79.093	145	1345	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_017316025.1	s__Enterococcus_C sp017316025	79.0271	72	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744115.1	s__Carnobacterium_A alterfunditum	78.7664	115	1345	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_001483965.1	s__Carnobacterium_A sp001483965	78.7184	139	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	98.95	98.95	0.90	0.90	2	-
GCA_017945845.1	s__WM01 sp017945845	78.4966	50	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__WM01	95.0	97.93	97.88	0.92	0.92	3	-
GCF_000744285.1	s__Carnobacterium_A pleistocenium	78.3436	127	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Carnobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111355.1	s__Isobaculum melis	78.2965	164	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Isobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730315.1	s__Enterococcus ureilyticus	77.5038	95	1345	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	99.76	99.29	0.97	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:45,971] [INFO] GTDB search result was written to GCF_000744375.1_ASM74437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:45,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:45,976] [INFO] DFAST_QC result json was written to GCF_000744375.1_ASM74437v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:45,976] [INFO] DFAST_QC completed!
[2024-01-24 15:11:45,976] [INFO] Total running time: 0h1m5s