[2023-06-13 11:30:29,720] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:30:29,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:30:29,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference
[2023-06-13 11:30:30,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:30:30,980] [INFO] Task started: Prodigal
[2023-06-13 11:30:30,980] [INFO] Running command: gunzip -c /var/lib/cwl/stge89486a8-688a-479a-a847-3d0d87aa7b23/GCA_003638855.1_ASM363885v1_genomic.fna.gz | prodigal -d GCA_003638855.1_ASM363885v1_genomic.fna/cds.fna -a GCA_003638855.1_ASM363885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:35,451] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:35,451] [INFO] Task started: HMMsearch
[2023-06-13 11:30:35,452] [INFO] Running command: hmmsearch --tblout GCA_003638855.1_ASM363885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/reference_markers.hmm GCA_003638855.1_ASM363885v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:35,657] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:35,658] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge89486a8-688a-479a-a847-3d0d87aa7b23/GCA_003638855.1_ASM363885v1_genomic.fna.gz]
[2023-06-13 11:30:35,688] [INFO] Query marker FASTA was written to GCA_003638855.1_ASM363885v1_genomic.fna/markers.fasta
[2023-06-13 11:30:35,689] [INFO] Task started: Blastn
[2023-06-13 11:30:35,689] [INFO] Running command: blastn -query GCA_003638855.1_ASM363885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/reference_markers.fasta -out GCA_003638855.1_ASM363885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:36,302] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:36,306] [INFO] Selected 16 target genomes.
[2023-06-13 11:30:36,307] [INFO] Target genome list was writen to GCA_003638855.1_ASM363885v1_genomic.fna/target_genomes.txt
[2023-06-13 11:30:36,312] [INFO] Task started: fastANI
[2023-06-13 11:30:36,312] [INFO] Running command: fastANI --query /var/lib/cwl/stge89486a8-688a-479a-a847-3d0d87aa7b23/GCA_003638855.1_ASM363885v1_genomic.fna.gz --refList GCA_003638855.1_ASM363885v1_genomic.fna/target_genomes.txt --output GCA_003638855.1_ASM363885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:42,252] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:42,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:42,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:42,258] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 11:30:42,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:30:42,258] [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	96.0324	264	360	95	conclusive
Abiotrophia defectiva	strain=ATCC 49176	GCA_000160075.2	46125	46125	type	True	95.8944	270	360	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 11:30:42,270] [INFO] DFAST Taxonomy check result was written to GCA_003638855.1_ASM363885v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:42,271] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:42,271] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:42,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/checkm_data
[2023-06-13 11:30:42,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:42,301] [INFO] Task started: CheckM
[2023-06-13 11:30:42,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003638855.1_ASM363885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003638855.1_ASM363885v1_genomic.fna/checkm_input GCA_003638855.1_ASM363885v1_genomic.fna/checkm_result
[2023-06-13 11:31:02,866] [INFO] Task succeeded: CheckM
[2023-06-13 11:31:02,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 12.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:31:02,901] [INFO] ===== Completeness check finished =====
[2023-06-13 11:31:02,901] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:31:02,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003638855.1_ASM363885v1_genomic.fna/markers.fasta)
[2023-06-13 11:31:02,902] [INFO] Task started: Blastn
[2023-06-13 11:31:02,902] [INFO] Running command: blastn -query GCA_003638855.1_ASM363885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0bba435-36b8-4de8-adad-ff60b27a3499/dqc_reference/reference_markers_gtdb.fasta -out GCA_003638855.1_ASM363885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:31:03,741] [INFO] Task succeeded: Blastn
[2023-06-13 11:31:03,744] [INFO] Selected 17 target genomes.
[2023-06-13 11:31:03,745] [INFO] Target genome list was writen to GCA_003638855.1_ASM363885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:31:03,772] [INFO] Task started: fastANI
[2023-06-13 11:31:03,772] [INFO] Running command: fastANI --query /var/lib/cwl/stge89486a8-688a-479a-a847-3d0d87aa7b23/GCA_003638855.1_ASM363885v1_genomic.fna.gz --refList GCA_003638855.1_ASM363885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003638855.1_ASM363885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:31:10,256] [INFO] Task succeeded: fastANI
[2023-06-13 11:31:10,260] [INFO] Found 2 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 11:31:10,260] [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_001815865.1	s__Abiotrophia sp001815865	97.036	266	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Abiotrophia	95.0	96.67	96.63	0.94	0.92	4	inconclusive
GCF_000160075.2	s__Abiotrophia defectiva	95.8944	270	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Abiotrophia	95.0	97.16	95.62	0.92	0.85	4	inconclusive
--------------------------------------------------------------------------------
[2023-06-13 11:31:10,262] [INFO] GTDB search result was written to GCA_003638855.1_ASM363885v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:31:10,262] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:31:10,265] [INFO] DFAST_QC result json was written to GCA_003638855.1_ASM363885v1_genomic.fna/dqc_result.json
[2023-06-13 11:31:10,265] [INFO] DFAST_QC completed!
[2023-06-13 11:31:10,265] [INFO] Total running time: 0h0m41s