[2024-01-24 14:19:59,755] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,757] [INFO] DQC Reference Directory: /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference
[2024-01-24 14:20:01,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,165] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,165] [INFO] Running command: gunzip -c /var/lib/cwl/stg182716c1-913b-4116-8af5-e4ba0cedbee8/GCF_019930605.1_ASM1993060v1_genomic.fna.gz | prodigal -d GCF_019930605.1_ASM1993060v1_genomic.fna/cds.fna -a GCF_019930605.1_ASM1993060v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:15,705] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:15,706] [INFO] Task started: HMMsearch
[2024-01-24 14:20:15,706] [INFO] Running command: hmmsearch --tblout GCF_019930605.1_ASM1993060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/reference_markers.hmm GCF_019930605.1_ASM1993060v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:15,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:15,950] [INFO] Found 6/6 markers.
[2024-01-24 14:20:15,976] [INFO] Query marker FASTA was written to GCF_019930605.1_ASM1993060v1_genomic.fna/markers.fasta
[2024-01-24 14:20:15,977] [INFO] Task started: Blastn
[2024-01-24 14:20:15,977] [INFO] Running command: blastn -query GCF_019930605.1_ASM1993060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/reference_markers.fasta -out GCF_019930605.1_ASM1993060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:16,624] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:16,627] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:16,627] [INFO] Target genome list was writen to GCF_019930605.1_ASM1993060v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:16,637] [INFO] Task started: fastANI
[2024-01-24 14:20:16,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg182716c1-913b-4116-8af5-e4ba0cedbee8/GCF_019930605.1_ASM1993060v1_genomic.fna.gz --refList GCF_019930605.1_ASM1993060v1_genomic.fna/target_genomes.txt --output GCF_019930605.1_ASM1993060v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:24,396] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:24,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:24,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:24,406] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:20:24,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:24,406] [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=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	100.0	890	890	95	conclusive
Prevotella nigrescens	strain=NCTC9336	GCA_900454985.1	28133	28133	type	True	99.9955	889	890	95	conclusive
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	99.8899	869	890	95	conclusive
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	86.5601	579	890	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	86.524	585	890	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	84.2638	570	890	95	below_threshold
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	84.1122	646	890	95	below_threshold
Prevotella pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	84.0878	638	890	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	79.0886	102	890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:24,408] [INFO] DFAST Taxonomy check result was written to GCF_019930605.1_ASM1993060v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:24,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:24,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:24,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/checkm_data
[2024-01-24 14:20:24,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:24,437] [INFO] Task started: CheckM
[2024-01-24 14:20:24,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930605.1_ASM1993060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930605.1_ASM1993060v1_genomic.fna/checkm_input GCF_019930605.1_ASM1993060v1_genomic.fna/checkm_result
[2024-01-24 14:21:08,701] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:08,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,723] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:08,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:08,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930605.1_ASM1993060v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:08,725] [INFO] Task started: Blastn
[2024-01-24 14:21:08,725] [INFO] Running command: blastn -query GCF_019930605.1_ASM1993060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga75190bd-a9a6-47b8-8fb2-404633603a11/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930605.1_ASM1993060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:09,686] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:09,695] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:09,695] [INFO] Target genome list was writen to GCF_019930605.1_ASM1993060v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:09,719] [INFO] Task started: fastANI
[2024-01-24 14:21:09,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg182716c1-913b-4116-8af5-e4ba0cedbee8/GCF_019930605.1_ASM1993060v1_genomic.fna.gz --refList GCF_019930605.1_ASM1993060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930605.1_ASM1993060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:15,384] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:15,392] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:15,392] [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	99.8899	869	890	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	86.5228	599	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000613945.1	s__Prevotella falsenii	84.2997	568	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220255.1	s__Prevotella pallens	84.0844	649	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000614025.1	s__Prevotella aurantiaca	81.6806	527	890	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	79.2746	193	890	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	79.0165	236	890	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	78.6598	127	890	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 14:21:15,394] [INFO] GTDB search result was written to GCF_019930605.1_ASM1993060v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:15,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:15,398] [INFO] DFAST_QC result json was written to GCF_019930605.1_ASM1993060v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:15,399] [INFO] DFAST_QC completed!
[2024-01-24 14:21:15,399] [INFO] Total running time: 0h1m16s