[2023-06-19 10:30:02,147] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:30:02,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:30:02,149] [INFO] DQC Reference Directory: /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference
[2023-06-19 10:30:03,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:30:03,533] [INFO] Task started: Prodigal
[2023-06-19 10:30:03,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ea3e569-f159-46dc-80cb-2646a436b396/GCA_014801245.1_ASM1480124v1_genomic.fna.gz | prodigal -d GCA_014801245.1_ASM1480124v1_genomic.fna/cds.fna -a GCA_014801245.1_ASM1480124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:30:11,102] [INFO] Task succeeded: Prodigal
[2023-06-19 10:30:11,102] [INFO] Task started: HMMsearch
[2023-06-19 10:30:11,103] [INFO] Running command: hmmsearch --tblout GCA_014801245.1_ASM1480124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/reference_markers.hmm GCA_014801245.1_ASM1480124v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:30:11,303] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:30:11,304] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9ea3e569-f159-46dc-80cb-2646a436b396/GCA_014801245.1_ASM1480124v1_genomic.fna.gz]
[2023-06-19 10:30:11,321] [INFO] Query marker FASTA was written to GCA_014801245.1_ASM1480124v1_genomic.fna/markers.fasta
[2023-06-19 10:30:11,321] [INFO] Task started: Blastn
[2023-06-19 10:30:11,321] [INFO] Running command: blastn -query GCA_014801245.1_ASM1480124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/reference_markers.fasta -out GCA_014801245.1_ASM1480124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:11,811] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:11,814] [INFO] Selected 11 target genomes.
[2023-06-19 10:30:11,815] [INFO] Target genome list was writen to GCA_014801245.1_ASM1480124v1_genomic.fna/target_genomes.txt
[2023-06-19 10:30:11,817] [INFO] Task started: fastANI
[2023-06-19 10:30:11,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea3e569-f159-46dc-80cb-2646a436b396/GCA_014801245.1_ASM1480124v1_genomic.fna.gz --refList GCA_014801245.1_ASM1480124v1_genomic.fna/target_genomes.txt --output GCA_014801245.1_ASM1480124v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:30:17,646] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:17,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:30:17,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:30:17,653] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:30:17,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:30:17,653] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	80.0267	222	484	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	79.4079	159	484	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.8038	69	484	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:30:17,655] [INFO] DFAST Taxonomy check result was written to GCA_014801245.1_ASM1480124v1_genomic.fna/tc_result.tsv
[2023-06-19 10:30:17,656] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:30:17,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:30:17,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/checkm_data
[2023-06-19 10:30:17,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:30:17,681] [INFO] Task started: CheckM
[2023-06-19 10:30:17,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014801245.1_ASM1480124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014801245.1_ASM1480124v1_genomic.fna/checkm_input GCA_014801245.1_ASM1480124v1_genomic.fna/checkm_result
[2023-06-19 10:30:46,685] [INFO] Task succeeded: CheckM
[2023-06-19 10:30:46,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:30:46,707] [INFO] ===== Completeness check finished =====
[2023-06-19 10:30:46,707] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:30:46,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014801245.1_ASM1480124v1_genomic.fna/markers.fasta)
[2023-06-19 10:30:46,708] [INFO] Task started: Blastn
[2023-06-19 10:30:46,708] [INFO] Running command: blastn -query GCA_014801245.1_ASM1480124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5b33ee9-1c3a-4420-b6f1-8c72bd82cf74/dqc_reference/reference_markers_gtdb.fasta -out GCA_014801245.1_ASM1480124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:47,175] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:47,178] [INFO] Selected 7 target genomes.
[2023-06-19 10:30:47,179] [INFO] Target genome list was writen to GCA_014801245.1_ASM1480124v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:30:47,184] [INFO] Task started: fastANI
[2023-06-19 10:30:47,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea3e569-f159-46dc-80cb-2646a436b396/GCA_014801245.1_ASM1480124v1_genomic.fna.gz --refList GCA_014801245.1_ASM1480124v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014801245.1_ASM1480124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:30:50,806] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:50,818] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:30:50,818] [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
GCA_014802345.1	s__Duncaniella sp014802345	97.819	398	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.04	97.99	0.90	0.88	3	conclusive
GCA_910577345.1	s__Duncaniella sp910577345	81.1875	264	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578445.1	s__Duncaniella sp910578445	80.2766	242	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801945.1	s__Duncaniella sp014801945	80.1035	208	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	97.85	97.85	0.77	0.77	2	-
GCF_004803915.1	s__Duncaniella dubosii	80.0267	222	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCA_910586665.1	s__Duncaniella sp910586665	79.9694	226	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544535.1	s__Duncaniella sp900544535	79.2446	188	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-19 10:30:50,820] [INFO] GTDB search result was written to GCA_014801245.1_ASM1480124v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:30:50,821] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:30:50,823] [INFO] DFAST_QC result json was written to GCA_014801245.1_ASM1480124v1_genomic.fna/dqc_result.json
[2023-06-19 10:30:50,824] [INFO] DFAST_QC completed!
[2023-06-19 10:30:50,824] [INFO] Total running time: 0h0m49s