[2024-01-24 12:44:33,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:33,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:33,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference
[2024-01-24 12:44:34,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:34,734] [INFO] Task started: Prodigal
[2024-01-24 12:44:34,735] [INFO] Running command: gunzip -c /var/lib/cwl/stga711f487-2ef1-4f52-bf57-f789804e3fde/GCF_014202695.1_ASM1420269v1_genomic.fna.gz | prodigal -d GCF_014202695.1_ASM1420269v1_genomic.fna/cds.fna -a GCF_014202695.1_ASM1420269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:40,781] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:40,782] [INFO] Task started: HMMsearch
[2024-01-24 12:44:40,782] [INFO] Running command: hmmsearch --tblout GCF_014202695.1_ASM1420269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/reference_markers.hmm GCF_014202695.1_ASM1420269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:40,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:40,966] [INFO] Found 6/6 markers.
[2024-01-24 12:44:40,988] [INFO] Query marker FASTA was written to GCF_014202695.1_ASM1420269v1_genomic.fna/markers.fasta
[2024-01-24 12:44:40,988] [INFO] Task started: Blastn
[2024-01-24 12:44:40,988] [INFO] Running command: blastn -query GCF_014202695.1_ASM1420269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/reference_markers.fasta -out GCF_014202695.1_ASM1420269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:41,581] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:41,585] [INFO] Selected 24 target genomes.
[2024-01-24 12:44:41,585] [INFO] Target genome list was writen to GCF_014202695.1_ASM1420269v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:41,873] [INFO] Task started: fastANI
[2024-01-24 12:44:41,873] [INFO] Running command: fastANI --query /var/lib/cwl/stga711f487-2ef1-4f52-bf57-f789804e3fde/GCF_014202695.1_ASM1420269v1_genomic.fna.gz --refList GCF_014202695.1_ASM1420269v1_genomic.fna/target_genomes.txt --output GCF_014202695.1_ASM1420269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:55,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:55,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:55,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:55,318] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:55,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:55,318] [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
Oribacterium sinus	strain=DSM 17245	GCA_014202695.1	237576	237576	type	True	100.0	895	897	95	conclusive
Oribacterium asaccharolyticum	strain=ACB7	GCA_000238075.1	1501332	1501332	type	True	82.1197	305	897	95	below_threshold
Oribacterium parvum	strain=ACB1	GCA_000238055.2	1501329	1501329	type	True	81.7916	329	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:55,320] [INFO] DFAST Taxonomy check result was written to GCF_014202695.1_ASM1420269v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:55,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:55,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:55,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/checkm_data
[2024-01-24 12:44:55,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:55,348] [INFO] Task started: CheckM
[2024-01-24 12:44:55,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202695.1_ASM1420269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202695.1_ASM1420269v1_genomic.fna/checkm_input GCF_014202695.1_ASM1420269v1_genomic.fna/checkm_result
[2024-01-24 12:45:18,168] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:18,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,192] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:18,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:18,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202695.1_ASM1420269v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:18,193] [INFO] Task started: Blastn
[2024-01-24 12:45:18,193] [INFO] Running command: blastn -query GCF_014202695.1_ASM1420269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ce0f8c-7ca9-41da-a5d0-0f791d5ca577/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202695.1_ASM1420269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:19,144] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:19,154] [INFO] Selected 22 target genomes.
[2024-01-24 12:45:19,155] [INFO] Target genome list was writen to GCF_014202695.1_ASM1420269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:19,207] [INFO] Task started: fastANI
[2024-01-24 12:45:19,207] [INFO] Running command: fastANI --query /var/lib/cwl/stga711f487-2ef1-4f52-bf57-f789804e3fde/GCF_014202695.1_ASM1420269v1_genomic.fna.gz --refList GCF_014202695.1_ASM1420269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202695.1_ASM1420269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:32,740] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:32,745] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:32,745] [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_014202695.1	s__Oribacterium sinus	100.0	895	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	95.41	95.16	0.92	0.89	5	conclusive
GCF_000238075.1	s__Oribacterium asaccharolyticum	82.0546	307	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	96.30	96.30	0.89	0.89	2	-
GCF_000238055.2	s__Oribacterium parvum	81.7393	332	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	98.88	98.13	0.97	0.97	3	-
GCA_015258095.1	s__Oribacterium sp015258095	78.8577	178	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:32,753] [INFO] GTDB search result was written to GCF_014202695.1_ASM1420269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:32,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:32,756] [INFO] DFAST_QC result json was written to GCF_014202695.1_ASM1420269v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:32,756] [INFO] DFAST_QC completed!
[2024-01-24 12:45:32,756] [INFO] Total running time: 0h0m59s