[2024-01-24 12:40:20,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,814] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference
[2024-01-24 12:40:22,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,014] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfd68bf2-65a5-4660-85ce-dfc6a4df6192/GCF_024499055.1_ASM2449905v1_genomic.fna.gz | prodigal -d GCF_024499055.1_ASM2449905v1_genomic.fna/cds.fna -a GCF_024499055.1_ASM2449905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:27,030] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:27,030] [INFO] Task started: HMMsearch
[2024-01-24 12:40:27,030] [INFO] Running command: hmmsearch --tblout GCF_024499055.1_ASM2449905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/reference_markers.hmm GCF_024499055.1_ASM2449905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:27,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:27,288] [INFO] Found 6/6 markers.
[2024-01-24 12:40:27,312] [INFO] Query marker FASTA was written to GCF_024499055.1_ASM2449905v1_genomic.fna/markers.fasta
[2024-01-24 12:40:27,313] [INFO] Task started: Blastn
[2024-01-24 12:40:27,313] [INFO] Running command: blastn -query GCF_024499055.1_ASM2449905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/reference_markers.fasta -out GCF_024499055.1_ASM2449905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:27,900] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:27,904] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:27,905] [INFO] Target genome list was writen to GCF_024499055.1_ASM2449905v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:27,913] [INFO] Task started: fastANI
[2024-01-24 12:40:27,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd68bf2-65a5-4660-85ce-dfc6a4df6192/GCF_024499055.1_ASM2449905v1_genomic.fna.gz --refList GCF_024499055.1_ASM2449905v1_genomic.fna/target_genomes.txt --output GCF_024499055.1_ASM2449905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:37,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:37,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:37,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:37,336] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:37,336] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:37,336] [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
Turicibacter bilis	strain=MMM721	GCA_024499055.1	2735723	2735723	type	True	100.0	924	928	95	conclusive
Turicibacter bilis	strain=MMM721	GCA_018305205.1	2735723	2735723	type	True	99.9369	862	928	95	conclusive
Turicibacter sanguinis	strain=MOL361	GCA_013046825.1	154288	154288	type	True	81.3222	445	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:37,338] [INFO] DFAST Taxonomy check result was written to GCF_024499055.1_ASM2449905v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:37,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:37,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:37,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/checkm_data
[2024-01-24 12:40:37,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:37,374] [INFO] Task started: CheckM
[2024-01-24 12:40:37,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024499055.1_ASM2449905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024499055.1_ASM2449905v1_genomic.fna/checkm_input GCF_024499055.1_ASM2449905v1_genomic.fna/checkm_result
[2024-01-24 12:40:59,284] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:59,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:59,305] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:59,306] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:59,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024499055.1_ASM2449905v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:59,307] [INFO] Task started: Blastn
[2024-01-24 12:40:59,307] [INFO] Running command: blastn -query GCF_024499055.1_ASM2449905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg452a659c-8d31-405d-9e12-c1c309a0e3ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_024499055.1_ASM2449905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:00,015] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:00,018] [INFO] Selected 15 target genomes.
[2024-01-24 12:41:00,018] [INFO] Target genome list was writen to GCF_024499055.1_ASM2449905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:00,029] [INFO] Task started: fastANI
[2024-01-24 12:41:00,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd68bf2-65a5-4660-85ce-dfc6a4df6192/GCF_024499055.1_ASM2449905v1_genomic.fna.gz --refList GCF_024499055.1_ASM2449905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024499055.1_ASM2449905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:07,727] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:07,733] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:07,733] [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_001543345.1	s__Turicibacter sp001543345	98.0421	775	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	98.30	97.82	0.87	0.78	10	conclusive
GCA_017888305.1	s__Turicibacter sp017888305	83.6805	386	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046825.1	s__Turicibacter sanguinis	81.3582	448	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.52	99.21	0.94	0.89	18	-
GCF_009935875.1	s__Turicibacter sp002311155	80.3079	325	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.25	99.25	0.93	0.91	3	-
GCA_002493395.1	s__Turicibacter sp002493395	79.9754	299	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486705.1	s__Turicibacter sp003486705	78.2632	184	928	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:07,735] [INFO] GTDB search result was written to GCF_024499055.1_ASM2449905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:07,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:07,738] [INFO] DFAST_QC result json was written to GCF_024499055.1_ASM2449905v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:07,739] [INFO] DFAST_QC completed!
[2024-01-24 12:41:07,739] [INFO] Total running time: 0h0m47s