[2024-01-25 18:59:36,271] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:36,277] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:36,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference
[2024-01-25 18:59:37,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:37,367] [INFO] Task started: Prodigal
[2024-01-25 18:59:37,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg652f0fd3-b92d-4f94-bae3-70d07fa39196/GCF_003130255.1_ASM313025v1_genomic.fna.gz | prodigal -d GCF_003130255.1_ASM313025v1_genomic.fna/cds.fna -a GCF_003130255.1_ASM313025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:42,878] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:42,878] [INFO] Task started: HMMsearch
[2024-01-25 18:59:42,878] [INFO] Running command: hmmsearch --tblout GCF_003130255.1_ASM313025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/reference_markers.hmm GCF_003130255.1_ASM313025v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:43,071] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:43,072] [INFO] Found 6/6 markers.
[2024-01-25 18:59:43,091] [INFO] Query marker FASTA was written to GCF_003130255.1_ASM313025v1_genomic.fna/markers.fasta
[2024-01-25 18:59:43,091] [INFO] Task started: Blastn
[2024-01-25 18:59:43,092] [INFO] Running command: blastn -query GCF_003130255.1_ASM313025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/reference_markers.fasta -out GCF_003130255.1_ASM313025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:43,748] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:43,751] [INFO] Selected 12 target genomes.
[2024-01-25 18:59:43,751] [INFO] Target genome list was writen to GCF_003130255.1_ASM313025v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:43,764] [INFO] Task started: fastANI
[2024-01-25 18:59:43,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg652f0fd3-b92d-4f94-bae3-70d07fa39196/GCF_003130255.1_ASM313025v1_genomic.fna.gz --refList GCF_003130255.1_ASM313025v1_genomic.fna/target_genomes.txt --output GCF_003130255.1_ASM313025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:51,238] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:51,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:51,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:51,245] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:51,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:51,245] [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
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	100.0	816	818	95	conclusive
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	94.0808	670	818	95	below_threshold
Aggregatibacter aphrophilus	strain=ATCC 33389	GCA_000226495.3	732	732	type	True	94.0252	660	818	95	below_threshold
Aggregatibacter segnis	strain=NCTC10977	GCA_900476035.1	739	739	type	True	86.5675	535	818	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	86.3766	534	818	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	81.6844	495	818	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	81.68	506	818	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.6985	236	818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:51,247] [INFO] DFAST Taxonomy check result was written to GCF_003130255.1_ASM313025v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:51,247] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:51,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:51,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/checkm_data
[2024-01-25 18:59:51,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:51,276] [INFO] Task started: CheckM
[2024-01-25 18:59:51,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003130255.1_ASM313025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003130255.1_ASM313025v1_genomic.fna/checkm_input GCF_003130255.1_ASM313025v1_genomic.fna/checkm_result
[2024-01-25 19:00:12,763] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:12,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:12,784] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:12,784] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:12,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003130255.1_ASM313025v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:12,785] [INFO] Task started: Blastn
[2024-01-25 19:00:12,785] [INFO] Running command: blastn -query GCF_003130255.1_ASM313025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04343b00-77db-422e-a2f6-24a01d7d9453/dqc_reference/reference_markers_gtdb.fasta -out GCF_003130255.1_ASM313025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:13,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:13,870] [INFO] Selected 9 target genomes.
[2024-01-25 19:00:13,870] [INFO] Target genome list was writen to GCF_003130255.1_ASM313025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:13,878] [INFO] Task started: fastANI
[2024-01-25 19:00:13,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg652f0fd3-b92d-4f94-bae3-70d07fa39196/GCF_003130255.1_ASM313025v1_genomic.fna.gz --refList GCF_003130255.1_ASM313025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003130255.1_ASM313025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:19,137] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:19,143] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:19,144] [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_003130255.1	s__Aggregatibacter kilianii	100.0	817	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	conclusive
GCF_900636915.1	s__Aggregatibacter aphrophilus	94.0853	671	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.58	96.00	0.94	0.87	19	-
GCF_000185305.1	s__Aggregatibacter segnis	86.3784	535	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.84	95.38	0.95	0.88	6	-
GCF_003130075.1	s__Aggregatibacter segnis_A	86.2623	521	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	-
GCF_017798005.1	s__Aggregatibacter sp000466335	85.8218	504	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.63	95.17	0.92	0.88	4	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	82.5949	612	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	82.5263	561	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	81.961	507	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	81.6841	494	818	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:19,146] [INFO] GTDB search result was written to GCF_003130255.1_ASM313025v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:19,146] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:19,149] [INFO] DFAST_QC result json was written to GCF_003130255.1_ASM313025v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:19,149] [INFO] DFAST_QC completed!
[2024-01-25 19:00:19,149] [INFO] Total running time: 0h0m43s