[2023-06-13 17:11:54,073] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:11:54,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:11:54,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference
[2023-06-13 17:11:55,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:11:55,431] [INFO] Task started: Prodigal
[2023-06-13 17:11:55,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg53362fdf-b1a6-4223-8e9f-9003a1c393c0/GCA_022646085.1_ASM2264608v1_genomic.fna.gz | prodigal -d GCA_022646085.1_ASM2264608v1_genomic.fna/cds.fna -a GCA_022646085.1_ASM2264608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:09,094] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:09,094] [INFO] Task started: HMMsearch
[2023-06-13 17:12:09,094] [INFO] Running command: hmmsearch --tblout GCA_022646085.1_ASM2264608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/reference_markers.hmm GCA_022646085.1_ASM2264608v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:09,361] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:09,362] [INFO] Found 6/6 markers.
[2023-06-13 17:12:09,393] [INFO] Query marker FASTA was written to GCA_022646085.1_ASM2264608v1_genomic.fna/markers.fasta
[2023-06-13 17:12:09,393] [INFO] Task started: Blastn
[2023-06-13 17:12:09,393] [INFO] Running command: blastn -query GCA_022646085.1_ASM2264608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/reference_markers.fasta -out GCA_022646085.1_ASM2264608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:10,008] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:10,013] [INFO] Selected 25 target genomes.
[2023-06-13 17:12:10,013] [INFO] Target genome list was writen to GCA_022646085.1_ASM2264608v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:10,020] [INFO] Task started: fastANI
[2023-06-13 17:12:10,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg53362fdf-b1a6-4223-8e9f-9003a1c393c0/GCA_022646085.1_ASM2264608v1_genomic.fna.gz --refList GCA_022646085.1_ASM2264608v1_genomic.fna/target_genomes.txt --output GCA_022646085.1_ASM2264608v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:23,577] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:23,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:23,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:23,583] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:23,584] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:12:23,584] [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
Prevotella cerevisiae	strain=DSM 100619	GCA_024054555.1	2053716	2053716	type	True	80.2904	423	941	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.7789	63	941	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.6845	66	941	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.4335	60	941	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:12:23,586] [INFO] DFAST Taxonomy check result was written to GCA_022646085.1_ASM2264608v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:23,586] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:23,587] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:23,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/checkm_data
[2023-06-13 17:12:23,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:23,622] [INFO] Task started: CheckM
[2023-06-13 17:12:23,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022646085.1_ASM2264608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022646085.1_ASM2264608v1_genomic.fna/checkm_input GCA_022646085.1_ASM2264608v1_genomic.fna/checkm_result
[2023-06-13 17:13:07,863] [INFO] Task succeeded: CheckM
[2023-06-13 17:13:07,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:13:07,888] [INFO] ===== Completeness check finished =====
[2023-06-13 17:13:07,888] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:13:07,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022646085.1_ASM2264608v1_genomic.fna/markers.fasta)
[2023-06-13 17:13:07,889] [INFO] Task started: Blastn
[2023-06-13 17:13:07,889] [INFO] Running command: blastn -query GCA_022646085.1_ASM2264608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933524df-fc83-4273-ae74-3668b8f1e400/dqc_reference/reference_markers_gtdb.fasta -out GCA_022646085.1_ASM2264608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:13:08,683] [INFO] Task succeeded: Blastn
[2023-06-13 17:13:08,688] [INFO] Selected 28 target genomes.
[2023-06-13 17:13:08,688] [INFO] Target genome list was writen to GCA_022646085.1_ASM2264608v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:13:08,696] [INFO] Task started: fastANI
[2023-06-13 17:13:08,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg53362fdf-b1a6-4223-8e9f-9003a1c393c0/GCA_022646085.1_ASM2264608v1_genomic.fna.gz --refList GCA_022646085.1_ASM2264608v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022646085.1_ASM2264608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:24,360] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:24,370] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:13:24,371] [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_002409785.1	s__Prevotella sp002409785	99.2745	744	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.35	99.13	0.87	0.82	3	conclusive
GCA_003483565.1	s__Prevotella sp003483565	78.5158	72	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCF_000426565.1	s__Prevotella albensis	76.7202	65	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000424185.1	s__Prevotella sp000424185	76.389	66	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249655.1	s__Prevotella sp900767615	76.3425	50	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:24,373] [INFO] GTDB search result was written to GCA_022646085.1_ASM2264608v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:24,374] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:24,377] [INFO] DFAST_QC result json was written to GCA_022646085.1_ASM2264608v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:24,377] [INFO] DFAST_QC completed!
[2023-06-13 17:13:24,378] [INFO] Total running time: 0h1m30s