[2024-01-24 11:59:11,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:11,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:11,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference
[2024-01-24 11:59:13,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:13,153] [INFO] Task started: Prodigal
[2024-01-24 11:59:13,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgeef4e2f0-eea4-478a-b709-47d4d9c03128/GCF_009906835.1_ASM990683v1_genomic.fna.gz | prodigal -d GCF_009906835.1_ASM990683v1_genomic.fna/cds.fna -a GCF_009906835.1_ASM990683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:17,867] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:17,867] [INFO] Task started: HMMsearch
[2024-01-24 11:59:17,868] [INFO] Running command: hmmsearch --tblout GCF_009906835.1_ASM990683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/reference_markers.hmm GCF_009906835.1_ASM990683v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:18,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:18,125] [INFO] Found 6/6 markers.
[2024-01-24 11:59:18,148] [INFO] Query marker FASTA was written to GCF_009906835.1_ASM990683v1_genomic.fna/markers.fasta
[2024-01-24 11:59:18,148] [INFO] Task started: Blastn
[2024-01-24 11:59:18,148] [INFO] Running command: blastn -query GCF_009906835.1_ASM990683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/reference_markers.fasta -out GCF_009906835.1_ASM990683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:18,807] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:18,811] [INFO] Selected 25 target genomes.
[2024-01-24 11:59:18,811] [INFO] Target genome list was writen to GCF_009906835.1_ASM990683v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:18,890] [INFO] Task started: fastANI
[2024-01-24 11:59:18,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef4e2f0-eea4-478a-b709-47d4d9c03128/GCF_009906835.1_ASM990683v1_genomic.fna.gz --refList GCF_009906835.1_ASM990683v1_genomic.fna/target_genomes.txt --output GCF_009906835.1_ASM990683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:29,622] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:29,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:29,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:29,628] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:29,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:29,628] [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
Swingsia samuiensis	strain=AH83	GCA_006542355.1	1293412	1293412	type	True	78.8791	60	673	95	below_threshold
Saccharibacter floricola	strain=DSM 15669	GCA_000378165.1	231053	231053	type	True	77.016	72	673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:29,630] [INFO] DFAST Taxonomy check result was written to GCF_009906835.1_ASM990683v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:29,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:29,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:29,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/checkm_data
[2024-01-24 11:59:29,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:29,658] [INFO] Task started: CheckM
[2024-01-24 11:59:29,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009906835.1_ASM990683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009906835.1_ASM990683v1_genomic.fna/checkm_input GCF_009906835.1_ASM990683v1_genomic.fna/checkm_result
[2024-01-24 11:59:50,493] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:50,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:50,529] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:50,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:50,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009906835.1_ASM990683v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:50,531] [INFO] Task started: Blastn
[2024-01-24 11:59:50,531] [INFO] Running command: blastn -query GCF_009906835.1_ASM990683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18766fe4-105c-42a8-bc3a-fef1f41bd9cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009906835.1_ASM990683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:51,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:51,669] [INFO] Selected 26 target genomes.
[2024-01-24 11:59:51,669] [INFO] Target genome list was writen to GCF_009906835.1_ASM990683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:51,710] [INFO] Task started: fastANI
[2024-01-24 11:59:51,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgeef4e2f0-eea4-478a-b709-47d4d9c03128/GCF_009906835.1_ASM990683v1_genomic.fna.gz --refList GCF_009906835.1_ASM990683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009906835.1_ASM990683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:04,018] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:04,023] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:04,023] [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_009906835.1	s__KACC-21507 sp009906835	100.0	672	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__KACC-21507	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006542355.1	s__Swingsia samuiensis	79.008	60	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swingsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834765.1	s__Saccharibacter sp009834765	77.6704	68	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	99.99	99.98	0.99	0.99	3	-
GCF_000378165.1	s__Saccharibacter floricola	77.016	72	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:04,025] [INFO] GTDB search result was written to GCF_009906835.1_ASM990683v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:04,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:04,029] [INFO] DFAST_QC result json was written to GCF_009906835.1_ASM990683v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:04,029] [INFO] DFAST_QC completed!
[2024-01-24 12:00:04,030] [INFO] Total running time: 0h0m52s