[2023-06-05 00:01:40,156] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:40,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:40,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference
[2023-06-05 00:01:41,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:41,422] [INFO] Task started: Prodigal
[2023-06-05 00:01:41,422] [INFO] Running command: gunzip -c /var/lib/cwl/stga31502d4-9602-4fb5-8657-b966cbad3d91/GCA_001769455.1_ASM176945v1_genomic.fna.gz | prodigal -d GCA_001769455.1_ASM176945v1_genomic.fna/cds.fna -a GCA_001769455.1_ASM176945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:51,386] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:51,386] [INFO] Task started: HMMsearch
[2023-06-05 00:01:51,386] [INFO] Running command: hmmsearch --tblout GCA_001769455.1_ASM176945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/reference_markers.hmm GCA_001769455.1_ASM176945v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:51,620] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:51,621] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga31502d4-9602-4fb5-8657-b966cbad3d91/GCA_001769455.1_ASM176945v1_genomic.fna.gz]
[2023-06-05 00:01:51,648] [INFO] Query marker FASTA was written to GCA_001769455.1_ASM176945v1_genomic.fna/markers.fasta
[2023-06-05 00:01:51,649] [INFO] Task started: Blastn
[2023-06-05 00:01:51,649] [INFO] Running command: blastn -query GCA_001769455.1_ASM176945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/reference_markers.fasta -out GCA_001769455.1_ASM176945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:01:52,239] [INFO] Task succeeded: Blastn
[2023-06-05 00:01:52,248] [INFO] Selected 10 target genomes.
[2023-06-05 00:01:52,248] [INFO] Target genome list was writen to GCA_001769455.1_ASM176945v1_genomic.fna/target_genomes.txt
[2023-06-05 00:01:52,253] [INFO] Task started: fastANI
[2023-06-05 00:01:52,253] [INFO] Running command: fastANI --query /var/lib/cwl/stga31502d4-9602-4fb5-8657-b966cbad3d91/GCA_001769455.1_ASM176945v1_genomic.fna.gz --refList GCA_001769455.1_ASM176945v1_genomic.fna/target_genomes.txt --output GCA_001769455.1_ASM176945v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:01:59,319] [INFO] Task succeeded: fastANI
[2023-06-05 00:01:59,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:01:59,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:01:59,321] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:01:59,321] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:01:59,322] [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
--------------------------------------------------------------------------------
[2023-06-05 00:01:59,324] [INFO] DFAST Taxonomy check result was written to GCA_001769455.1_ASM176945v1_genomic.fna/tc_result.tsv
[2023-06-05 00:01:59,324] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:01:59,325] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:01:59,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/checkm_data
[2023-06-05 00:01:59,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:01:59,355] [INFO] Task started: CheckM
[2023-06-05 00:01:59,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001769455.1_ASM176945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001769455.1_ASM176945v1_genomic.fna/checkm_input GCA_001769455.1_ASM176945v1_genomic.fna/checkm_result
[2023-06-05 00:02:33,645] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:33,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:33,668] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:33,668] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:33,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001769455.1_ASM176945v1_genomic.fna/markers.fasta)
[2023-06-05 00:02:33,669] [INFO] Task started: Blastn
[2023-06-05 00:02:33,669] [INFO] Running command: blastn -query GCA_001769455.1_ASM176945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36af777-c82b-42f7-bcc1-2a449867c4f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_001769455.1_ASM176945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:34,357] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:34,363] [INFO] Selected 11 target genomes.
[2023-06-05 00:02:34,363] [INFO] Target genome list was writen to GCA_001769455.1_ASM176945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:34,519] [INFO] Task started: fastANI
[2023-06-05 00:02:34,519] [INFO] Running command: fastANI --query /var/lib/cwl/stga31502d4-9602-4fb5-8657-b966cbad3d91/GCA_001769455.1_ASM176945v1_genomic.fna.gz --refList GCA_001769455.1_ASM176945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001769455.1_ASM176945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:40,871] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:40,879] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:02:40,879] [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_001769215.1	s__UBA6244 sp001769215	99.7509	590	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6244	95.0	99.75	99.75	0.99	0.99	2	conclusive
GCA_002840975.1	s__UBA6244 sp002840975	93.9898	491	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6244	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002771745.1	s__UBA6244 sp002771745	92.6538	475	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6244	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440885.1	s__UBA6244 sp002440885	76.8055	89	597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6244	95.0	96.99	96.99	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:40,881] [INFO] GTDB search result was written to GCA_001769455.1_ASM176945v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:40,882] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:40,884] [INFO] DFAST_QC result json was written to GCA_001769455.1_ASM176945v1_genomic.fna/dqc_result.json
[2023-06-05 00:02:40,885] [INFO] DFAST_QC completed!
[2023-06-05 00:02:40,885] [INFO] Total running time: 0h1m1s