[2023-06-13 04:12:52,970] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:12:52,979] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:12:52,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference
[2023-06-13 04:12:54,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:12:54,387] [INFO] Task started: Prodigal
[2023-06-13 04:12:54,387] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6ca0cff-078e-474f-898a-df1c8f0d4418/GCA_022655375.1_ASM2265537v1_genomic.fna.gz | prodigal -d GCA_022655375.1_ASM2265537v1_genomic.fna/cds.fna -a GCA_022655375.1_ASM2265537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:13:04,651] [INFO] Task succeeded: Prodigal
[2023-06-13 04:13:04,652] [INFO] Task started: HMMsearch
[2023-06-13 04:13:04,652] [INFO] Running command: hmmsearch --tblout GCA_022655375.1_ASM2265537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/reference_markers.hmm GCA_022655375.1_ASM2265537v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:13:04,866] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:13:04,867] [INFO] Found 6/6 markers.
[2023-06-13 04:13:04,889] [INFO] Query marker FASTA was written to GCA_022655375.1_ASM2265537v1_genomic.fna/markers.fasta
[2023-06-13 04:13:04,890] [INFO] Task started: Blastn
[2023-06-13 04:13:04,890] [INFO] Running command: blastn -query GCA_022655375.1_ASM2265537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/reference_markers.fasta -out GCA_022655375.1_ASM2265537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:13:05,492] [INFO] Task succeeded: Blastn
[2023-06-13 04:13:05,500] [INFO] Selected 21 target genomes.
[2023-06-13 04:13:05,500] [INFO] Target genome list was writen to GCA_022655375.1_ASM2265537v1_genomic.fna/target_genomes.txt
[2023-06-13 04:13:05,501] [INFO] Task started: fastANI
[2023-06-13 04:13:05,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ca0cff-078e-474f-898a-df1c8f0d4418/GCA_022655375.1_ASM2265537v1_genomic.fna.gz --refList GCA_022655375.1_ASM2265537v1_genomic.fna/target_genomes.txt --output GCA_022655375.1_ASM2265537v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:13:19,792] [INFO] Task succeeded: fastANI
[2023-06-13 04:13:19,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:13:19,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:13:19,797] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:13:19,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:13:19,797] [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	79.9144	309	680	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:13:19,800] [INFO] DFAST Taxonomy check result was written to GCA_022655375.1_ASM2265537v1_genomic.fna/tc_result.tsv
[2023-06-13 04:13:19,801] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:13:19,801] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:13:19,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/checkm_data
[2023-06-13 04:13:19,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:13:19,833] [INFO] Task started: CheckM
[2023-06-13 04:13:19,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022655375.1_ASM2265537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022655375.1_ASM2265537v1_genomic.fna/checkm_input GCA_022655375.1_ASM2265537v1_genomic.fna/checkm_result
[2023-06-13 04:13:55,228] [INFO] Task succeeded: CheckM
[2023-06-13 04:13:55,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:13:55,252] [INFO] ===== Completeness check finished =====
[2023-06-13 04:13:55,252] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:13:55,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022655375.1_ASM2265537v1_genomic.fna/markers.fasta)
[2023-06-13 04:13:55,253] [INFO] Task started: Blastn
[2023-06-13 04:13:55,253] [INFO] Running command: blastn -query GCA_022655375.1_ASM2265537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80dd1162-45c3-46ef-8357-8ca643b0e5c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022655375.1_ASM2265537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:13:56,148] [INFO] Task succeeded: Blastn
[2023-06-13 04:13:56,153] [INFO] Selected 23 target genomes.
[2023-06-13 04:13:56,154] [INFO] Target genome list was writen to GCA_022655375.1_ASM2265537v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:13:56,156] [INFO] Task started: fastANI
[2023-06-13 04:13:56,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ca0cff-078e-474f-898a-df1c8f0d4418/GCA_022655375.1_ASM2265537v1_genomic.fna.gz --refList GCA_022655375.1_ASM2265537v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022655375.1_ASM2265537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:14:06,561] [INFO] Task succeeded: fastANI
[2023-06-13 04:14:06,570] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:14:06,570] [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	99.3764	580	680	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	78.4832	62	680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCF_000424185.1	s__Prevotella sp000424185	76.7034	50	680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:14:06,572] [INFO] GTDB search result was written to GCA_022655375.1_ASM2265537v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:14:06,573] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:14:06,576] [INFO] DFAST_QC result json was written to GCA_022655375.1_ASM2265537v1_genomic.fna/dqc_result.json
[2023-06-13 04:14:06,577] [INFO] DFAST_QC completed!
[2023-06-13 04:14:06,577] [INFO] Total running time: 0h1m14s