[2024-01-24 13:31:33,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference
[2024-01-24 13:31:34,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,969] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgf53675fd-51cf-44e5-9e08-ef0848b2c02a/GCF_006542355.1_ASM654235v1_genomic.fna.gz | prodigal -d GCF_006542355.1_ASM654235v1_genomic.fna/cds.fna -a GCF_006542355.1_ASM654235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:40,453] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:40,454] [INFO] Task started: HMMsearch
[2024-01-24 13:31:40,454] [INFO] Running command: hmmsearch --tblout GCF_006542355.1_ASM654235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/reference_markers.hmm GCF_006542355.1_ASM654235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:40,700] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:40,702] [INFO] Found 6/6 markers.
[2024-01-24 13:31:40,724] [INFO] Query marker FASTA was written to GCF_006542355.1_ASM654235v1_genomic.fna/markers.fasta
[2024-01-24 13:31:40,725] [INFO] Task started: Blastn
[2024-01-24 13:31:40,725] [INFO] Running command: blastn -query GCF_006542355.1_ASM654235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/reference_markers.fasta -out GCF_006542355.1_ASM654235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:41,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:41,438] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:41,439] [INFO] Target genome list was writen to GCF_006542355.1_ASM654235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:41,453] [INFO] Task started: fastANI
[2024-01-24 13:31:41,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53675fd-51cf-44e5-9e08-ef0848b2c02a/GCF_006542355.1_ASM654235v1_genomic.fna.gz --refList GCF_006542355.1_ASM654235v1_genomic.fna/target_genomes.txt --output GCF_006542355.1_ASM654235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:49,282] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:49,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:49,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:49,287] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:49,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:49,287] [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	100.0	729	731	95	conclusive
Neokomagataea tanensis	strain=AH13 = NBRC 106556	GCA_006542335.1	661191	661191	type	True	79.1555	69	731	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	76.9831	78	731	95	below_threshold
Neokomagataea thailandica	strain=NBRC 106555	GCA_001598495.1	661190	661190	type	True	76.8186	78	731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:49,289] [INFO] DFAST Taxonomy check result was written to GCF_006542355.1_ASM654235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:49,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:49,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:49,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/checkm_data
[2024-01-24 13:31:49,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:49,314] [INFO] Task started: CheckM
[2024-01-24 13:31:49,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542355.1_ASM654235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542355.1_ASM654235v1_genomic.fna/checkm_input GCF_006542355.1_ASM654235v1_genomic.fna/checkm_result
[2024-01-24 13:32:13,100] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:13,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,125] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:13,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:13,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542355.1_ASM654235v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:13,127] [INFO] Task started: Blastn
[2024-01-24 13:32:13,127] [INFO] Running command: blastn -query GCF_006542355.1_ASM654235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c1c35b2-aa0a-41f2-836c-6e66f06593a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542355.1_ASM654235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:14,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:14,183] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:14,183] [INFO] Target genome list was writen to GCF_006542355.1_ASM654235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:14,240] [INFO] Task started: fastANI
[2024-01-24 13:32:14,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53675fd-51cf-44e5-9e08-ef0848b2c02a/GCF_006542355.1_ASM654235v1_genomic.fna.gz --refList GCF_006542355.1_ASM654235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006542355.1_ASM654235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:22,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:22,607] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:22,607] [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_006542355.1	s__Swingsia samuiensis	100.0	727	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swingsia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001787335.1	s__Kozakia baliensis	78.9221	53	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Kozakia	95.0	98.19	97.27	0.93	0.89	4	-
GCF_006542335.1	s__Neokomagataea tanensis	78.7149	68	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906835.1	s__KACC-21507 sp009906835	78.2544	59	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__KACC-21507	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834805.1	s__Saccharibacter sp009834805	77.5105	55	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Saccharibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122595.1	s__Neokomagataea sp018122595	77.012	78	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598495.1	s__Neokomagataea thailandica	76.7885	79	731	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Neokomagataea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:22,609] [INFO] GTDB search result was written to GCF_006542355.1_ASM654235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:22,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:22,613] [INFO] DFAST_QC result json was written to GCF_006542355.1_ASM654235v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:22,613] [INFO] DFAST_QC completed!
[2024-01-24 13:32:22,613] [INFO] Total running time: 0h0m49s