[2024-01-24 13:01:19,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,234] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference
[2024-01-24 13:01:20,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,438] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg85b9a920-3ae0-4c29-af28-108734aa4e27/GCF_900454985.1_53750_E01_genomic.fna.gz | prodigal -d GCF_900454985.1_53750_E01_genomic.fna/cds.fna -a GCF_900454985.1_53750_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:34,720] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:34,720] [INFO] Task started: HMMsearch
[2024-01-24 13:01:34,720] [INFO] Running command: hmmsearch --tblout GCF_900454985.1_53750_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/reference_markers.hmm GCF_900454985.1_53750_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,955] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,988] [INFO] Query marker FASTA was written to GCF_900454985.1_53750_E01_genomic.fna/markers.fasta
[2024-01-24 13:01:34,989] [INFO] Task started: Blastn
[2024-01-24 13:01:34,989] [INFO] Running command: blastn -query GCF_900454985.1_53750_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/reference_markers.fasta -out GCF_900454985.1_53750_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:35,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:35,563] [INFO] Selected 10 target genomes.
[2024-01-24 13:01:35,563] [INFO] Target genome list was writen to GCF_900454985.1_53750_E01_genomic.fna/target_genomes.txt
[2024-01-24 13:01:35,569] [INFO] Task started: fastANI
[2024-01-24 13:01:35,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b9a920-3ae0-4c29-af28-108734aa4e27/GCF_900454985.1_53750_E01_genomic.fna.gz --refList GCF_900454985.1_53750_E01_genomic.fna/target_genomes.txt --output GCF_900454985.1_53750_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:42,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:42,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:42,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:42,247] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:01:42,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:42,247] [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 nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	100.0	901	903	95	conclusive
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	99.9956	890	903	95	conclusive
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	99.9083	866	903	95	conclusive
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	86.3022	594	903	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	86.289	590	903	95	below_threshold
Prevotella pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	84.321	628	903	95	below_threshold
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	84.2734	654	903	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	84.1043	570	903	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.057	95	903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:42,249] [INFO] DFAST Taxonomy check result was written to GCF_900454985.1_53750_E01_genomic.fna/tc_result.tsv
[2024-01-24 13:01:42,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:42,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:42,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/checkm_data
[2024-01-24 13:01:42,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:42,279] [INFO] Task started: CheckM
[2024-01-24 13:01:42,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454985.1_53750_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454985.1_53750_E01_genomic.fna/checkm_input GCF_900454985.1_53750_E01_genomic.fna/checkm_result
[2024-01-24 13:02:24,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:24,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:24,402] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:24,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:24,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454985.1_53750_E01_genomic.fna/markers.fasta)
[2024-01-24 13:02:24,403] [INFO] Task started: Blastn
[2024-01-24 13:02:24,404] [INFO] Running command: blastn -query GCF_900454985.1_53750_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ed5c7a9-9585-44aa-94e4-3992697c9dc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454985.1_53750_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:25,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:25,145] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:25,145] [INFO] Target genome list was writen to GCF_900454985.1_53750_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:25,161] [INFO] Task started: fastANI
[2024-01-24 13:02:25,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b9a920-3ae0-4c29-af28-108734aa4e27/GCF_900454985.1_53750_E01_genomic.fna.gz --refList GCF_900454985.1_53750_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454985.1_53750_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:30,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:30,673] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:30,673] [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_000220235.1	s__Prevotella nigrescens	99.9083	866	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	conclusive
GCF_001953955.1	s__Prevotella intermedia	86.4375	597	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000220255.1	s__Prevotella pallens	84.2863	654	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000613945.1	s__Prevotella falsenii	84.07	572	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614025.1	s__Prevotella aurantiaca	81.7631	531	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000688375.1	s__Prevotella sp000688375	79.5191	193	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155655.1	s__Prevotella ihumii	79.2028	226	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614065.1	s__Prevotella dentasini	79.0188	120	903	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:30,675] [INFO] GTDB search result was written to GCF_900454985.1_53750_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:30,675] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:30,680] [INFO] DFAST_QC result json was written to GCF_900454985.1_53750_E01_genomic.fna/dqc_result.json
[2024-01-24 13:02:30,680] [INFO] DFAST_QC completed!
[2024-01-24 13:02:30,680] [INFO] Total running time: 0h1m11s