[2024-01-24 14:40:02,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,367] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference
[2024-01-24 14:40:03,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,731] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbe02515-74f2-4006-ad76-5898d1b7db11/GCF_018390735.1_ASM1839073v1_genomic.fna.gz | prodigal -d GCF_018390735.1_ASM1839073v1_genomic.fna/cds.fna -a GCF_018390735.1_ASM1839073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:14,797] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:14,797] [INFO] Task started: HMMsearch
[2024-01-24 14:40:14,798] [INFO] Running command: hmmsearch --tblout GCF_018390735.1_ASM1839073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/reference_markers.hmm GCF_018390735.1_ASM1839073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:15,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:15,088] [INFO] Found 6/6 markers.
[2024-01-24 14:40:15,128] [INFO] Query marker FASTA was written to GCF_018390735.1_ASM1839073v1_genomic.fna/markers.fasta
[2024-01-24 14:40:15,128] [INFO] Task started: Blastn
[2024-01-24 14:40:15,128] [INFO] Running command: blastn -query GCF_018390735.1_ASM1839073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/reference_markers.fasta -out GCF_018390735.1_ASM1839073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:15,804] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:15,810] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:15,810] [INFO] Target genome list was writen to GCF_018390735.1_ASM1839073v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:15,823] [INFO] Task started: fastANI
[2024-01-24 14:40:15,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe02515-74f2-4006-ad76-5898d1b7db11/GCF_018390735.1_ASM1839073v1_genomic.fna.gz --refList GCF_018390735.1_ASM1839073v1_genomic.fna/target_genomes.txt --output GCF_018390735.1_ASM1839073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:27,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:27,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:27,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:27,072] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:27,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:27,073] [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
Fusibacter paucivorans	strain=DSM 12116	GCA_018390735.1	76009	76009	type	True	100.0	1425	1431	95	conclusive
Fusibacter ferrireducens	strain=Q10-2	GCA_015352425.1	2785058	2785058	type	True	77.5471	84	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:27,077] [INFO] DFAST Taxonomy check result was written to GCF_018390735.1_ASM1839073v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:27,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:27,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:27,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/checkm_data
[2024-01-24 14:40:27,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:27,130] [INFO] Task started: CheckM
[2024-01-24 14:40:27,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018390735.1_ASM1839073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018390735.1_ASM1839073v1_genomic.fna/checkm_input GCF_018390735.1_ASM1839073v1_genomic.fna/checkm_result
[2024-01-24 14:41:05,274] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:05,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:05,296] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:05,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:05,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018390735.1_ASM1839073v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:05,298] [INFO] Task started: Blastn
[2024-01-24 14:41:05,298] [INFO] Running command: blastn -query GCF_018390735.1_ASM1839073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a74b84d-767a-4351-896f-8ef5c7322d19/dqc_reference/reference_markers_gtdb.fasta -out GCF_018390735.1_ASM1839073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:06,312] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:06,322] [INFO] Selected 23 target genomes.
[2024-01-24 14:41:06,323] [INFO] Target genome list was writen to GCF_018390735.1_ASM1839073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:06,340] [INFO] Task started: fastANI
[2024-01-24 14:41:06,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe02515-74f2-4006-ad76-5898d1b7db11/GCF_018390735.1_ASM1839073v1_genomic.fna.gz --refList GCF_018390735.1_ASM1839073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018390735.1_ASM1839073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:18,659] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:18,664] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:18,664] [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_018390735.1	s__Fusibacter paucivorans	100.0	1425	1431	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015352425.1	s__Fusibacter_A sp015352425	77.5471	84	1431	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748365.1	s__Fusibacter_A sp001748365	77.168	81	1431	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452745.1	s__Fusibacter_A sp002452745	76.8409	71	1431	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:18,666] [INFO] GTDB search result was written to GCF_018390735.1_ASM1839073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:18,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:18,669] [INFO] DFAST_QC result json was written to GCF_018390735.1_ASM1839073v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:18,669] [INFO] DFAST_QC completed!
[2024-01-24 14:41:18,669] [INFO] Total running time: 0h1m16s