[2024-01-24 13:22:02,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference
[2024-01-24 13:22:03,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,580] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,580] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eaf7360-2f43-44a3-a9fd-6d9ebf4e2669/GCF_003290385.1_ASM329038v1_genomic.fna.gz | prodigal -d GCF_003290385.1_ASM329038v1_genomic.fna/cds.fna -a GCF_003290385.1_ASM329038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,616] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,617] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,617] [INFO] Running command: hmmsearch --tblout GCF_003290385.1_ASM329038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/reference_markers.hmm GCF_003290385.1_ASM329038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:08,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:08,881] [INFO] Found 6/6 markers.
[2024-01-24 13:22:08,907] [INFO] Query marker FASTA was written to GCF_003290385.1_ASM329038v1_genomic.fna/markers.fasta
[2024-01-24 13:22:08,908] [INFO] Task started: Blastn
[2024-01-24 13:22:08,908] [INFO] Running command: blastn -query GCF_003290385.1_ASM329038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/reference_markers.fasta -out GCF_003290385.1_ASM329038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:09,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:09,640] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:09,640] [INFO] Target genome list was writen to GCF_003290385.1_ASM329038v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:09,649] [INFO] Task started: fastANI
[2024-01-24 13:22:09,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eaf7360-2f43-44a3-a9fd-6d9ebf4e2669/GCF_003290385.1_ASM329038v1_genomic.fna.gz --refList GCF_003290385.1_ASM329038v1_genomic.fna/target_genomes.txt --output GCF_003290385.1_ASM329038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:17,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:17,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:17,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:17,554] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:22:17,555] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:22:17,555] [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
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	100.0	769	772	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	99.9945	770	772	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	98.4027	654	772	95	inconclusive
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	96.6369	676	772	95	inconclusive
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	88.8393	593	772	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	88.7733	590	772	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	88.418	580	772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:17,562] [INFO] DFAST Taxonomy check result was written to GCF_003290385.1_ASM329038v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:17,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:17,563] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:17,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/checkm_data
[2024-01-24 13:22:17,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:17,597] [INFO] Task started: CheckM
[2024-01-24 13:22:17,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003290385.1_ASM329038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003290385.1_ASM329038v1_genomic.fna/checkm_input GCF_003290385.1_ASM329038v1_genomic.fna/checkm_result
[2024-01-24 13:22:40,625] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:40,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,643] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:40,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:40,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003290385.1_ASM329038v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:40,645] [INFO] Task started: Blastn
[2024-01-24 13:22:40,645] [INFO] Running command: blastn -query GCF_003290385.1_ASM329038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3082f9c-cb8e-4fe1-ad9d-64a9c87d241e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003290385.1_ASM329038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:41,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:41,792] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:41,792] [INFO] Target genome list was writen to GCF_003290385.1_ASM329038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:41,799] [INFO] Task started: fastANI
[2024-01-24 13:22:41,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eaf7360-2f43-44a3-a9fd-6d9ebf4e2669/GCF_003290385.1_ASM329038v1_genomic.fna.gz --refList GCF_003290385.1_ASM329038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003290385.1_ASM329038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:45,905] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:45,911] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:45,912] [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_900444945.1	s__Actinobacillus lignieresii	96.6363	676	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	conclusive
GCF_000739435.1	s__Actinobacillus suis	88.8102	590	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_900636745.1	s__Actinobacillus equuli	88.4019	580	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000374285.1	s__Actinobacillus capsulatus	87.4442	577	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188255.1	s__Actinobacillus ureae	87.3421	573	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_901687125.1	s__Actinobacillus vicugnae	81.9366	523	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:45,913] [INFO] GTDB search result was written to GCF_003290385.1_ASM329038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:45,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:45,916] [INFO] DFAST_QC result json was written to GCF_003290385.1_ASM329038v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:45,916] [INFO] DFAST_QC completed!
[2024-01-24 13:22:45,916] [INFO] Total running time: 0h0m44s