[2024-01-24 13:56:13,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference
[2024-01-24 13:56:14,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,462] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,462] [INFO] Running command: gunzip -c /var/lib/cwl/stg46c5a50b-0ce5-490c-8b49-0a7fc8f05d51/GCF_000613945.1_ASM61394v1_genomic.fna.gz | prodigal -d GCF_000613945.1_ASM61394v1_genomic.fna/cds.fna -a GCF_000613945.1_ASM61394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:29,476] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:29,477] [INFO] Task started: HMMsearch
[2024-01-24 13:56:29,477] [INFO] Running command: hmmsearch --tblout GCF_000613945.1_ASM61394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/reference_markers.hmm GCF_000613945.1_ASM61394v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:29,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:29,748] [INFO] Found 6/6 markers.
[2024-01-24 13:56:29,786] [INFO] Query marker FASTA was written to GCF_000613945.1_ASM61394v1_genomic.fna/markers.fasta
[2024-01-24 13:56:29,787] [INFO] Task started: Blastn
[2024-01-24 13:56:29,787] [INFO] Running command: blastn -query GCF_000613945.1_ASM61394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/reference_markers.fasta -out GCF_000613945.1_ASM61394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:30,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:30,428] [INFO] Selected 8 target genomes.
[2024-01-24 13:56:30,429] [INFO] Target genome list was writen to GCF_000613945.1_ASM61394v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:30,443] [INFO] Task started: fastANI
[2024-01-24 13:56:30,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c5a50b-0ce5-490c-8b49-0a7fc8f05d51/GCF_000613945.1_ASM61394v1_genomic.fna.gz --refList GCF_000613945.1_ASM61394v1_genomic.fna/target_genomes.txt --output GCF_000613945.1_ASM61394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:40,230] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:40,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:40,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:40,242] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:40,243] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:40,243] [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 falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	100.0	887	889	95	conclusive
Prevotella intermedia	strain=NCTC13070	GCA_900455005.1	28131	28131	type	True	90.1689	699	889	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	90.138	713	889	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	90.1089	700	889	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	90.0874	709	889	95	below_threshold
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	83.9468	580	889	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9101	58	889	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:40,245] [INFO] DFAST Taxonomy check result was written to GCF_000613945.1_ASM61394v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:40,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:40,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:40,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/checkm_data
[2024-01-24 13:56:40,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:40,275] [INFO] Task started: CheckM
[2024-01-24 13:56:40,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613945.1_ASM61394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613945.1_ASM61394v1_genomic.fna/checkm_input GCF_000613945.1_ASM61394v1_genomic.fna/checkm_result
[2024-01-24 13:57:24,761] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:24,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:24,785] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:24,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:24,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613945.1_ASM61394v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:24,786] [INFO] Task started: Blastn
[2024-01-24 13:57:24,787] [INFO] Running command: blastn -query GCF_000613945.1_ASM61394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg094fa1b7-ed36-4259-b6e8-1b283bc097f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613945.1_ASM61394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:25,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:25,634] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:25,634] [INFO] Target genome list was writen to GCF_000613945.1_ASM61394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:25,641] [INFO] Task started: fastANI
[2024-01-24 13:57:25,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c5a50b-0ce5-490c-8b49-0a7fc8f05d51/GCF_000613945.1_ASM61394v1_genomic.fna.gz --refList GCF_000613945.1_ASM61394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613945.1_ASM61394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:33,628] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:33,641] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:33,641] [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_000613945.1	s__Prevotella falsenii	100.0	887	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001953955.1	s__Prevotella intermedia	90.1249	713	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000220235.1	s__Prevotella nigrescens	83.9474	568	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_000614025.1	s__Prevotella aurantiaca	82.2137	552	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000220255.1	s__Prevotella pallens	79.8155	452	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_900155655.1	s__Prevotella ihumii	79.3064	272	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262015.1	s__Prevotella fusca	78.9037	130	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000688375.1	s__Prevotella sp000688375	78.6124	236	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440225.1	s__Prevotella sp002440225	76.288	54	889	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.88	98.88	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:33,643] [INFO] GTDB search result was written to GCF_000613945.1_ASM61394v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:33,643] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:33,647] [INFO] DFAST_QC result json was written to GCF_000613945.1_ASM61394v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:33,647] [INFO] DFAST_QC completed!
[2024-01-24 13:57:33,647] [INFO] Total running time: 0h1m20s