[2024-01-24 11:35:23,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference
[2024-01-24 11:35:26,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,249] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg2920b23b-3100-4779-ab76-dfbc6727c2c1/GCF_000178495.2_ASM17849v2_genomic.fna.gz | prodigal -d GCF_000178495.2_ASM17849v2_genomic.fna/cds.fna -a GCF_000178495.2_ASM17849v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,308] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,309] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,309] [INFO] Running command: hmmsearch --tblout GCF_000178495.2_ASM17849v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/reference_markers.hmm GCF_000178495.2_ASM17849v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:31,590] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:31,592] [INFO] Found 6/6 markers.
[2024-01-24 11:35:31,627] [INFO] Query marker FASTA was written to GCF_000178495.2_ASM17849v2_genomic.fna/markers.fasta
[2024-01-24 11:35:31,627] [INFO] Task started: Blastn
[2024-01-24 11:35:31,628] [INFO] Running command: blastn -query GCF_000178495.2_ASM17849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/reference_markers.fasta -out GCF_000178495.2_ASM17849v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,006] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,010] [INFO] Selected 12 target genomes.
[2024-01-24 11:35:33,011] [INFO] Target genome list was writen to GCF_000178495.2_ASM17849v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,039] [INFO] Task started: fastANI
[2024-01-24 11:35:33,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2920b23b-3100-4779-ab76-dfbc6727c2c1/GCF_000178495.2_ASM17849v2_genomic.fna.gz --refList GCF_000178495.2_ASM17849v2_genomic.fna/target_genomes.txt --output GCF_000178495.2_ASM17849v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:40,632] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:40,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:40,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:40,644] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:40,645] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:40,645] [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=4074	GCA_000178495.2	715	715	type	True	100.0	769	772	95	inconclusive
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	99.9945	770	772	95	inconclusive
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	98.4033	653	772	95	inconclusive
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	96.6221	676	772	95	inconclusive
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	88.8104	592	772	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	88.7426	592	772	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	88.42	580	772	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:40,647] [INFO] DFAST Taxonomy check result was written to GCF_000178495.2_ASM17849v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:40,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:40,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:40,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/checkm_data
[2024-01-24 11:35:40,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:40,673] [INFO] Task started: CheckM
[2024-01-24 11:35:40,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000178495.2_ASM17849v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000178495.2_ASM17849v2_genomic.fna/checkm_input GCF_000178495.2_ASM17849v2_genomic.fna/checkm_result
[2024-01-24 11:36:03,030] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:03,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:03,048] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:03,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:03,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000178495.2_ASM17849v2_genomic.fna/markers.fasta)
[2024-01-24 11:36:03,049] [INFO] Task started: Blastn
[2024-01-24 11:36:03,049] [INFO] Running command: blastn -query GCF_000178495.2_ASM17849v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e1ad411-67f9-475c-9bb3-07f06eedaa3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000178495.2_ASM17849v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:04,099] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:04,103] [INFO] Selected 6 target genomes.
[2024-01-24 11:36:04,103] [INFO] Target genome list was writen to GCF_000178495.2_ASM17849v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:04,110] [INFO] Task started: fastANI
[2024-01-24 11:36:04,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg2920b23b-3100-4779-ab76-dfbc6727c2c1/GCF_000178495.2_ASM17849v2_genomic.fna.gz --refList GCF_000178495.2_ASM17849v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000178495.2_ASM17849v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:07,964] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:07,975] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:07,975] [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	96.6157	675	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	88.723	593	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	88.42	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	87.4532	578	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	87.3626	571	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	81.9781	520	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 11:36:07,977] [INFO] GTDB search result was written to GCF_000178495.2_ASM17849v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:07,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:07,981] [INFO] DFAST_QC result json was written to GCF_000178495.2_ASM17849v2_genomic.fna/dqc_result.json
[2024-01-24 11:36:07,982] [INFO] DFAST_QC completed!
[2024-01-24 11:36:07,982] [INFO] Total running time: 0h0m44s