[2024-01-24 13:27:58,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference
[2024-01-24 13:27:59,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,889] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,890] [INFO] Running command: gunzip -c /var/lib/cwl/stge1724600-b672-4264-98a2-774c316e0e37/GCF_000374285.1_ASM37428v1_genomic.fna.gz | prodigal -d GCF_000374285.1_ASM37428v1_genomic.fna/cds.fna -a GCF_000374285.1_ASM37428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:05,386] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:05,387] [INFO] Task started: HMMsearch
[2024-01-24 13:28:05,387] [INFO] Running command: hmmsearch --tblout GCF_000374285.1_ASM37428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/reference_markers.hmm GCF_000374285.1_ASM37428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:05,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:05,637] [INFO] Found 6/6 markers.
[2024-01-24 13:28:05,661] [INFO] Query marker FASTA was written to GCF_000374285.1_ASM37428v1_genomic.fna/markers.fasta
[2024-01-24 13:28:05,662] [INFO] Task started: Blastn
[2024-01-24 13:28:05,662] [INFO] Running command: blastn -query GCF_000374285.1_ASM37428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/reference_markers.fasta -out GCF_000374285.1_ASM37428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:06,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:06,371] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:06,371] [INFO] Target genome list was writen to GCF_000374285.1_ASM37428v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:06,725] [INFO] Task started: fastANI
[2024-01-24 13:28:06,725] [INFO] Running command: fastANI --query /var/lib/cwl/stge1724600-b672-4264-98a2-774c316e0e37/GCF_000374285.1_ASM37428v1_genomic.fna.gz --refList GCF_000374285.1_ASM37428v1_genomic.fna/target_genomes.txt --output GCF_000374285.1_ASM37428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:14,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:14,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:14,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:14,733] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:14,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:14,734] [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 capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	100.0	844	851	95	conclusive
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	93.0736	691	851	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	92.4724	697	851	95	below_threshold
Actinobacillus suis	strain=NCTC12996	GCA_900187155.1	716	716	type	True	92.3996	697	851	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	91.7511	660	851	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	87.3415	589	851	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	87.3402	589	851	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	87.3273	540	851	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	77.8868	147	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:14,735] [INFO] DFAST Taxonomy check result was written to GCF_000374285.1_ASM37428v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:14,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:14,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:14,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/checkm_data
[2024-01-24 13:28:14,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:14,769] [INFO] Task started: CheckM
[2024-01-24 13:28:14,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374285.1_ASM37428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374285.1_ASM37428v1_genomic.fna/checkm_input GCF_000374285.1_ASM37428v1_genomic.fna/checkm_result
[2024-01-24 13:28:39,296] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:39,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:39,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:39,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:39,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374285.1_ASM37428v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:39,318] [INFO] Task started: Blastn
[2024-01-24 13:28:39,318] [INFO] Running command: blastn -query GCF_000374285.1_ASM37428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28f3e1de-9c7b-4bfc-a5e6-a2cbf3c768df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374285.1_ASM37428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:40,561] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:40,567] [INFO] Selected 6 target genomes.
[2024-01-24 13:28:40,568] [INFO] Target genome list was writen to GCF_000374285.1_ASM37428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:40,585] [INFO] Task started: fastANI
[2024-01-24 13:28:40,585] [INFO] Running command: fastANI --query /var/lib/cwl/stge1724600-b672-4264-98a2-774c316e0e37/GCF_000374285.1_ASM37428v1_genomic.fna.gz --refList GCF_000374285.1_ASM37428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374285.1_ASM37428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:44,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:44,802] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:44,802] [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_000374285.1	s__Actinobacillus capsulatus	100.0	846	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900636745.1	s__Actinobacillus equuli	93.0736	691	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_000739435.1	s__Actinobacillus suis	92.4722	697	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_000188255.1	s__Actinobacillus ureae	91.7511	660	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_900444945.1	s__Actinobacillus lignieresii	87.1025	571	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_901687125.1	s__Actinobacillus vicugnae	83.0765	608	851	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 13:28:44,805] [INFO] GTDB search result was written to GCF_000374285.1_ASM37428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:44,805] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:44,808] [INFO] DFAST_QC result json was written to GCF_000374285.1_ASM37428v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:44,808] [INFO] DFAST_QC completed!
[2024-01-24 13:28:44,808] [INFO] Total running time: 0h0m46s