[2024-01-24 12:31:19,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:19,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:19,769] [INFO] DQC Reference Directory: /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference
[2024-01-24 12:31:21,036] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:21,037] [INFO] Task started: Prodigal
[2024-01-24 12:31:21,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg71bd04a1-eb71-4ac5-892c-f9dc4db55757/GCF_000613405.1_ASM61340v1_genomic.fna.gz | prodigal -d GCF_000613405.1_ASM61340v1_genomic.fna/cds.fna -a GCF_000613405.1_ASM61340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:36,672] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:36,673] [INFO] Task started: HMMsearch
[2024-01-24 12:31:36,673] [INFO] Running command: hmmsearch --tblout GCF_000613405.1_ASM61340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/reference_markers.hmm GCF_000613405.1_ASM61340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:36,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:36,883] [INFO] Found 6/6 markers.
[2024-01-24 12:31:36,908] [INFO] Query marker FASTA was written to GCF_000613405.1_ASM61340v1_genomic.fna/markers.fasta
[2024-01-24 12:31:36,908] [INFO] Task started: Blastn
[2024-01-24 12:31:36,908] [INFO] Running command: blastn -query GCF_000613405.1_ASM61340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/reference_markers.fasta -out GCF_000613405.1_ASM61340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:37,509] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:37,513] [INFO] Selected 18 target genomes.
[2024-01-24 12:31:37,513] [INFO] Target genome list was writen to GCF_000613405.1_ASM61340v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:37,521] [INFO] Task started: fastANI
[2024-01-24 12:31:37,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bd04a1-eb71-4ac5-892c-f9dc4db55757/GCF_000613405.1_ASM61340v1_genomic.fna.gz --refList GCF_000613405.1_ASM61340v1_genomic.fna/target_genomes.txt --output GCF_000613405.1_ASM61340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:46,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:46,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:46,435] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:46,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:46,436] [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 enoeca	strain=JCM 12259	GCA_000613405.1	76123	76123	type	True	100.0	863	867	95	conclusive
Prevotella pleuritidis	strain=JCM 14110	GCA_000613725.1	407975	407975	type	True	87.2305	506	867	95	below_threshold
Prevotella oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	84.9174	103	867	95	below_threshold
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	84.5866	108	867	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	82.1994	78	867	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	81.6858	76	867	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	81.2505	108	867	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	81.1404	100	867	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	79.829	68	867	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	78.855	72	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,438] [INFO] DFAST Taxonomy check result was written to GCF_000613405.1_ASM61340v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:46,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:46,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:46,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/checkm_data
[2024-01-24 12:31:46,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:46,467] [INFO] Task started: CheckM
[2024-01-24 12:31:46,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613405.1_ASM61340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613405.1_ASM61340v1_genomic.fna/checkm_input GCF_000613405.1_ASM61340v1_genomic.fna/checkm_result
[2024-01-24 12:32:32,221] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:32,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:32,241] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:32,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:32,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613405.1_ASM61340v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:32,242] [INFO] Task started: Blastn
[2024-01-24 12:32:32,242] [INFO] Running command: blastn -query GCF_000613405.1_ASM61340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76f3f8a-5175-44cb-9318-5125190ba3df/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613405.1_ASM61340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:33,085] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:33,091] [INFO] Selected 25 target genomes.
[2024-01-24 12:32:33,091] [INFO] Target genome list was writen to GCF_000613405.1_ASM61340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:33,119] [INFO] Task started: fastANI
[2024-01-24 12:32:33,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bd04a1-eb71-4ac5-892c-f9dc4db55757/GCF_000613405.1_ASM61340v1_genomic.fna.gz --refList GCF_000613405.1_ASM61340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613405.1_ASM61340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:45,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:45,449] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:45,449] [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_000613405.1	s__Prevotella enoeca	100.0	863	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_000613725.1	s__Prevotella pleuritidis	87.2559	505	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.65	0.96	0.96	4	-
GCF_000382385.1	s__Prevotella maculosa	81.3038	106	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000177075.1	s__Prevotella buccalis	79.9683	83	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000688375.1	s__Prevotella sp000688375	78.8905	78	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016901395.1	s__Prevotella sp016901395	78.2268	60	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185145.2	s__Prevotella oralis	78.198	68	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.13	0.96	0.92	6	-
GCA_900547005.1	s__Prevotella sp900547005	77.1911	53	867	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.66	96.14	0.84	0.69	4	-
GCA_905373605.1	s__Prevotella sp905373605	76.165	54	867	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 12:32:45,450] [INFO] GTDB search result was written to GCF_000613405.1_ASM61340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:45,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:45,454] [INFO] DFAST_QC result json was written to GCF_000613405.1_ASM61340v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:45,454] [INFO] DFAST_QC completed!
[2024-01-24 12:32:45,454] [INFO] Total running time: 0h1m26s