[2024-01-25 19:34:20,963] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:20,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:20,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference
[2024-01-25 19:34:22,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,112] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,113] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcbc7ab4-5527-476a-91ee-8d188ea1c6b8/GCF_013267415.1_ASM1326741v1_genomic.fna.gz | prodigal -d GCF_013267415.1_ASM1326741v1_genomic.fna/cds.fna -a GCF_013267415.1_ASM1326741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:26,286] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:26,286] [INFO] Task started: HMMsearch
[2024-01-25 19:34:26,286] [INFO] Running command: hmmsearch --tblout GCF_013267415.1_ASM1326741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/reference_markers.hmm GCF_013267415.1_ASM1326741v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:26,481] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:26,482] [INFO] Found 6/6 markers.
[2024-01-25 19:34:26,500] [INFO] Query marker FASTA was written to GCF_013267415.1_ASM1326741v1_genomic.fna/markers.fasta
[2024-01-25 19:34:26,500] [INFO] Task started: Blastn
[2024-01-25 19:34:26,500] [INFO] Running command: blastn -query GCF_013267415.1_ASM1326741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/reference_markers.fasta -out GCF_013267415.1_ASM1326741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:27,012] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:27,015] [INFO] Selected 22 target genomes.
[2024-01-25 19:34:27,015] [INFO] Target genome list was writen to GCF_013267415.1_ASM1326741v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:27,021] [INFO] Task started: fastANI
[2024-01-25 19:34:27,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbc7ab4-5527-476a-91ee-8d188ea1c6b8/GCF_013267415.1_ASM1326741v1_genomic.fna.gz --refList GCF_013267415.1_ASM1326741v1_genomic.fna/target_genomes.txt --output GCF_013267415.1_ASM1326741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:36,287] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:36,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:36,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:36,291] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:34:36,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:36,292] [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
Abiotrophia defectiva	strain=FDAARGOS_785	GCA_013267415.1	46125	46125	type	True	100.0	681	682	95	conclusive
Abiotrophia defectiva	strain=ATCC 49176	GCA_000160075.2	46125	46125	type	True	99.9809	675	682	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:34:36,293] [INFO] DFAST Taxonomy check result was written to GCF_013267415.1_ASM1326741v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:36,293] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:36,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:36,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/checkm_data
[2024-01-25 19:34:36,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:36,317] [INFO] Task started: CheckM
[2024-01-25 19:34:36,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013267415.1_ASM1326741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013267415.1_ASM1326741v1_genomic.fna/checkm_input GCF_013267415.1_ASM1326741v1_genomic.fna/checkm_result
[2024-01-25 19:34:54,995] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:54,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:55,010] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:55,010] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:55,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013267415.1_ASM1326741v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:55,011] [INFO] Task started: Blastn
[2024-01-25 19:34:55,011] [INFO] Running command: blastn -query GCF_013267415.1_ASM1326741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3307791-2f2b-41fa-b0b8-8f4ea596f20d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013267415.1_ASM1326741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:55,748] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:55,751] [INFO] Selected 21 target genomes.
[2024-01-25 19:34:55,752] [INFO] Target genome list was writen to GCF_013267415.1_ASM1326741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:55,762] [INFO] Task started: fastANI
[2024-01-25 19:34:55,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbc7ab4-5527-476a-91ee-8d188ea1c6b8/GCF_013267415.1_ASM1326741v1_genomic.fna.gz --refList GCF_013267415.1_ASM1326741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013267415.1_ASM1326741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:03,641] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:03,643] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:03,643] [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_000160075.2	s__Abiotrophia defectiva	99.9809	675	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Abiotrophia	95.0	97.16	95.62	0.92	0.85	4	conclusive
GCF_001815865.1	s__Abiotrophia sp001815865	94.4349	594	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Abiotrophia	95.0	96.67	96.63	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:03,646] [INFO] GTDB search result was written to GCF_013267415.1_ASM1326741v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:03,646] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:03,648] [INFO] DFAST_QC result json was written to GCF_013267415.1_ASM1326741v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:03,648] [INFO] DFAST_QC completed!
[2024-01-25 19:35:03,649] [INFO] Total running time: 0h0m43s