[2024-01-24 13:02:03,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference
[2024-01-24 13:02:05,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,179] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,179] [INFO] Running command: gunzip -c /var/lib/cwl/stga20f7772-ebd6-4a43-9d16-e069943874c9/GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/cds.fna -a GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:07,842] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:07,843] [INFO] Task started: HMMsearch
[2024-01-24 13:02:07,843] [INFO] Running command: hmmsearch --tblout GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/reference_markers.hmm GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:08,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:08,121] [INFO] Found 6/6 markers.
[2024-01-24 13:02:08,139] [INFO] Query marker FASTA was written to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:02:08,139] [INFO] Task started: Blastn
[2024-01-24 13:02:08,140] [INFO] Running command: blastn -query GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/reference_markers.fasta -out GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:08,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:08,741] [INFO] Selected 25 target genomes.
[2024-01-24 13:02:08,741] [INFO] Target genome list was writen to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:02:08,751] [INFO] Task started: fastANI
[2024-01-24 13:02:08,751] [INFO] Running command: fastANI --query /var/lib/cwl/stga20f7772-ebd6-4a43-9d16-e069943874c9/GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna.gz --refList GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:17,671] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:17,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:17,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:17,683] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:17,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:17,683] [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
Aerococcus suis	strain=DSM 21500	GCA_900176325.1	371602	371602	type	True	100.0	452	453	95	conclusive
Aerococcus viridans	strain=NCTC8251	GCA_900445095.1	1377	1377	suspected-type	True	82.0839	55	453	95	below_threshold
Aerococcus viridans	strain=CCUG4311	GCA_001543285.1	1377	1377	suspected-type	True	81.7118	55	453	95	below_threshold
Aerococcus urinaeequi	strain=CCUG28094	GCA_001543205.1	51665	51665	type	True	78.3143	61	453	95	below_threshold
Aerococcus urinaeequi	strain=DSM 20341	GCA_000425085.1	51665	51665	suspected-type	True	78.1205	60	453	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:17,685] [INFO] DFAST Taxonomy check result was written to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:17,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:17,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:17,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/checkm_data
[2024-01-24 13:02:17,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:17,704] [INFO] Task started: CheckM
[2024-01-24 13:02:17,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/checkm_input GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:34,029] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:34,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,056] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:34,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:34,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:34,057] [INFO] Task started: Blastn
[2024-01-24 13:02:34,057] [INFO] Running command: blastn -query GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c2b2f4-54a3-4e65-b704-87944a1402f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:34,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:34,841] [INFO] Selected 22 target genomes.
[2024-01-24 13:02:34,841] [INFO] Target genome list was writen to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:34,855] [INFO] Task started: fastANI
[2024-01-24 13:02:34,856] [INFO] Running command: fastANI --query /var/lib/cwl/stga20f7772-ebd6-4a43-9d16-e069943874c9/GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna.gz --refList GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:43,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:43,976] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:43,976] [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_900176325.1	s__Aerococcus suis	100.0	452	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002083135.2	s__Aerococcus viridans_C	79.6583	62	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797145.1	s__Aerococcus sp003797145	79.3428	57	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252085.1	s__Aerococcus sp002252085	79.2995	63	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543205.1	s__Aerococcus urinaeequi	78.3767	60	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	96.56	95.91	0.88	0.83	18	-
GCF_002871935.1	s__Aerococcus viridans_B	78.3523	65	453	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	98.96	98.96	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:43,979] [INFO] GTDB search result was written to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:43,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:43,984] [INFO] DFAST_QC result json was written to GCF_900176325.1_IMG-taxon_2622736423_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:43,984] [INFO] DFAST_QC completed!
[2024-01-24 13:02:43,984] [INFO] Total running time: 0h0m40s