[2023-06-19 00:04:42,796] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:04:42,800] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:04:42,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference
[2023-06-19 00:04:44,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:04:44,968] [INFO] Task started: Prodigal
[2023-06-19 00:04:44,968] [INFO] Running command: gunzip -c /var/lib/cwl/stgb16cac8b-b4b8-47ed-a631-65be10aa94ce/GCA_018698355.1_ASM1869835v1_genomic.fna.gz | prodigal -d GCA_018698355.1_ASM1869835v1_genomic.fna/cds.fna -a GCA_018698355.1_ASM1869835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:04:53,834] [INFO] Task succeeded: Prodigal
[2023-06-19 00:04:53,834] [INFO] Task started: HMMsearch
[2023-06-19 00:04:53,835] [INFO] Running command: hmmsearch --tblout GCA_018698355.1_ASM1869835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/reference_markers.hmm GCA_018698355.1_ASM1869835v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:04:54,100] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:04:54,101] [INFO] Found 6/6 markers.
[2023-06-19 00:04:54,133] [INFO] Query marker FASTA was written to GCA_018698355.1_ASM1869835v1_genomic.fna/markers.fasta
[2023-06-19 00:04:54,133] [INFO] Task started: Blastn
[2023-06-19 00:04:54,133] [INFO] Running command: blastn -query GCA_018698355.1_ASM1869835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/reference_markers.fasta -out GCA_018698355.1_ASM1869835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:04:54,750] [INFO] Task succeeded: Blastn
[2023-06-19 00:04:54,755] [INFO] Selected 25 target genomes.
[2023-06-19 00:04:54,756] [INFO] Target genome list was writen to GCA_018698355.1_ASM1869835v1_genomic.fna/target_genomes.txt
[2023-06-19 00:04:54,757] [INFO] Task started: fastANI
[2023-06-19 00:04:54,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16cac8b-b4b8-47ed-a631-65be10aa94ce/GCA_018698355.1_ASM1869835v1_genomic.fna.gz --refList GCA_018698355.1_ASM1869835v1_genomic.fna/target_genomes.txt --output GCA_018698355.1_ASM1869835v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:09,733] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:09,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:09,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:09,736] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:05:09,736] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:05:09,737] [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
--------------------------------------------------------------------------------
[2023-06-19 00:05:09,739] [INFO] DFAST Taxonomy check result was written to GCA_018698355.1_ASM1869835v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:09,740] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:09,740] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:09,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/checkm_data
[2023-06-19 00:05:09,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:09,773] [INFO] Task started: CheckM
[2023-06-19 00:05:09,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018698355.1_ASM1869835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018698355.1_ASM1869835v1_genomic.fna/checkm_input GCA_018698355.1_ASM1869835v1_genomic.fna/checkm_result
[2023-06-19 00:05:41,165] [INFO] Task succeeded: CheckM
[2023-06-19 00:05:41,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:05:41,213] [INFO] ===== Completeness check finished =====
[2023-06-19 00:05:41,214] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:05:41,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018698355.1_ASM1869835v1_genomic.fna/markers.fasta)
[2023-06-19 00:05:41,215] [INFO] Task started: Blastn
[2023-06-19 00:05:41,215] [INFO] Running command: blastn -query GCA_018698355.1_ASM1869835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c97093-5f96-4487-b307-fe85e6fbb7b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018698355.1_ASM1869835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:41,969] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:41,980] [INFO] Selected 24 target genomes.
[2023-06-19 00:05:41,980] [INFO] Target genome list was writen to GCA_018698355.1_ASM1869835v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:05:41,987] [INFO] Task started: fastANI
[2023-06-19 00:05:41,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16cac8b-b4b8-47ed-a631-65be10aa94ce/GCA_018698355.1_ASM1869835v1_genomic.fna.gz --refList GCA_018698355.1_ASM1869835v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018698355.1_ASM1869835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:05:55,179] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:55,196] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:05:55,196] [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_018661505.1	s__GCA-002708315 sp018661505	99.9245	736	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	conclusive
GCA_002708315.1	s__GCA-002708315 sp002708315	91.2208	559	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686705.1	s__GCA-002708315 sp002686705	77.8517	88	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845105.1	s__GCA-002708315 sp016845105	77.1993	137	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203805.1	s__GCA-002708315 sp013203805	76.3573	120	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:05:55,199] [INFO] GTDB search result was written to GCA_018698355.1_ASM1869835v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:05:55,200] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:05:55,206] [INFO] DFAST_QC result json was written to GCA_018698355.1_ASM1869835v1_genomic.fna/dqc_result.json
[2023-06-19 00:05:55,206] [INFO] DFAST_QC completed!
[2023-06-19 00:05:55,206] [INFO] Total running time: 0h1m12s