[2023-06-17 14:42:35,466] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:42:35,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:42:35,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference
[2023-06-17 14:42:36,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:42:36,689] [INFO] Task started: Prodigal
[2023-06-17 14:42:36,689] [INFO] Running command: gunzip -c /var/lib/cwl/stged7256cd-dd4a-4a61-bc43-4f838955cf65/GCA_028708535.1_ASM2870853v1_genomic.fna.gz | prodigal -d GCA_028708535.1_ASM2870853v1_genomic.fna/cds.fna -a GCA_028708535.1_ASM2870853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:42:43,167] [INFO] Task succeeded: Prodigal
[2023-06-17 14:42:43,168] [INFO] Task started: HMMsearch
[2023-06-17 14:42:43,168] [INFO] Running command: hmmsearch --tblout GCA_028708535.1_ASM2870853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/reference_markers.hmm GCA_028708535.1_ASM2870853v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:42:43,410] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:42:43,412] [INFO] Found 6/6 markers.
[2023-06-17 14:42:43,437] [INFO] Query marker FASTA was written to GCA_028708535.1_ASM2870853v1_genomic.fna/markers.fasta
[2023-06-17 14:42:43,437] [INFO] Task started: Blastn
[2023-06-17 14:42:43,437] [INFO] Running command: blastn -query GCA_028708535.1_ASM2870853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/reference_markers.fasta -out GCA_028708535.1_ASM2870853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:42:44,026] [INFO] Task succeeded: Blastn
[2023-06-17 14:42:44,048] [INFO] Selected 23 target genomes.
[2023-06-17 14:42:44,048] [INFO] Target genome list was writen to GCA_028708535.1_ASM2870853v1_genomic.fna/target_genomes.txt
[2023-06-17 14:42:44,052] [INFO] Task started: fastANI
[2023-06-17 14:42:44,052] [INFO] Running command: fastANI --query /var/lib/cwl/stged7256cd-dd4a-4a61-bc43-4f838955cf65/GCA_028708535.1_ASM2870853v1_genomic.fna.gz --refList GCA_028708535.1_ASM2870853v1_genomic.fna/target_genomes.txt --output GCA_028708535.1_ASM2870853v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:42:57,136] [INFO] Task succeeded: fastANI
[2023-06-17 14:42:57,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:42:57,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:42:57,141] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:42:57,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:42:57,141] [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
Bacteroides coprosuis	strain=DSM 18011	GCA_000212915.1	151276	151276	type	True	76.6148	68	694	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:42:57,144] [INFO] DFAST Taxonomy check result was written to GCA_028708535.1_ASM2870853v1_genomic.fna/tc_result.tsv
[2023-06-17 14:42:57,144] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:42:57,144] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:42:57,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/checkm_data
[2023-06-17 14:42:57,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:42:57,174] [INFO] Task started: CheckM
[2023-06-17 14:42:57,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708535.1_ASM2870853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708535.1_ASM2870853v1_genomic.fna/checkm_input GCA_028708535.1_ASM2870853v1_genomic.fna/checkm_result
[2023-06-17 14:43:22,006] [INFO] Task succeeded: CheckM
[2023-06-17 14:43:22,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:43:22,025] [INFO] ===== Completeness check finished =====
[2023-06-17 14:43:22,026] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:43:22,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708535.1_ASM2870853v1_genomic.fna/markers.fasta)
[2023-06-17 14:43:22,026] [INFO] Task started: Blastn
[2023-06-17 14:43:22,027] [INFO] Running command: blastn -query GCA_028708535.1_ASM2870853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb4d5fdf-0a3a-4f48-b424-d968f186b042/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708535.1_ASM2870853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:22,770] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:22,775] [INFO] Selected 26 target genomes.
[2023-06-17 14:43:22,775] [INFO] Target genome list was writen to GCA_028708535.1_ASM2870853v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:43:22,793] [INFO] Task started: fastANI
[2023-06-17 14:43:22,793] [INFO] Running command: fastANI --query /var/lib/cwl/stged7256cd-dd4a-4a61-bc43-4f838955cf65/GCA_028708535.1_ASM2870853v1_genomic.fna.gz --refList GCA_028708535.1_ASM2870853v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708535.1_ASM2870853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:43:37,333] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:37,339] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:43:37,339] [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
GCA_012518235.1	s__JAAYSY01 sp012518235	99.3516	506	694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__JAAYSY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000212915.1	s__Bacteroides_E coprosuis	76.5914	66	694	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:43:37,341] [INFO] GTDB search result was written to GCA_028708535.1_ASM2870853v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:43:37,342] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:43:37,345] [INFO] DFAST_QC result json was written to GCA_028708535.1_ASM2870853v1_genomic.fna/dqc_result.json
[2023-06-17 14:43:37,345] [INFO] DFAST_QC completed!
[2023-06-17 14:43:37,345] [INFO] Total running time: 0h1m2s