[2024-01-24 13:31:26,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:26,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:26,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference
[2024-01-24 13:31:27,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:27,397] [INFO] Task started: Prodigal
[2024-01-24 13:31:27,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f29eca8-648d-4891-90d6-1cbb8576996a/GCF_003201715.1_ASM320171v1_genomic.fna.gz | prodigal -d GCF_003201715.1_ASM320171v1_genomic.fna/cds.fna -a GCF_003201715.1_ASM320171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:47,080] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:47,081] [INFO] Task started: HMMsearch
[2024-01-24 13:31:47,081] [INFO] Running command: hmmsearch --tblout GCF_003201715.1_ASM320171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/reference_markers.hmm GCF_003201715.1_ASM320171v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:47,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:47,338] [INFO] Found 6/6 markers.
[2024-01-24 13:31:47,365] [INFO] Query marker FASTA was written to GCF_003201715.1_ASM320171v1_genomic.fna/markers.fasta
[2024-01-24 13:31:47,366] [INFO] Task started: Blastn
[2024-01-24 13:31:47,366] [INFO] Running command: blastn -query GCF_003201715.1_ASM320171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/reference_markers.fasta -out GCF_003201715.1_ASM320171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:47,945] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:47,950] [INFO] Selected 11 target genomes.
[2024-01-24 13:31:47,950] [INFO] Target genome list was writen to GCF_003201715.1_ASM320171v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:47,955] [INFO] Task started: fastANI
[2024-01-24 13:31:47,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f29eca8-648d-4891-90d6-1cbb8576996a/GCF_003201715.1_ASM320171v1_genomic.fna.gz --refList GCF_003201715.1_ASM320171v1_genomic.fna/target_genomes.txt --output GCF_003201715.1_ASM320171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:55,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:55,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:55,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:55,065] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:31:55,065] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:55,065] [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 shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	100.0	1116	1120	95	conclusive
Prevotella shahii	strain=JCM 12083	GCA_000613445.1	228603	228603	type	True	99.8876	1065	1120	95	conclusive
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	81.9774	712	1120	95	below_threshold
Prevotella loescheii	strain=JCM 12249	GCA_000613485.1	840	840	type	True	81.9451	713	1120	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	81.9137	731	1120	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	79.1311	51	1120	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	78.2511	63	1120	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	77.6695	54	1120	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.2087	58	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:55,068] [INFO] DFAST Taxonomy check result was written to GCF_003201715.1_ASM320171v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:55,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:55,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:55,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/checkm_data
[2024-01-24 13:31:55,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:55,107] [INFO] Task started: CheckM
[2024-01-24 13:31:55,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201715.1_ASM320171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201715.1_ASM320171v1_genomic.fna/checkm_input GCF_003201715.1_ASM320171v1_genomic.fna/checkm_result
[2024-01-24 13:32:50,699] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:50,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:50,742] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:50,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:50,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201715.1_ASM320171v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:50,743] [INFO] Task started: Blastn
[2024-01-24 13:32:50,744] [INFO] Running command: blastn -query GCF_003201715.1_ASM320171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg932f7ef5-e76a-4e88-819a-38d4c37f0c7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201715.1_ASM320171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,536] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:51,537] [INFO] Target genome list was writen to GCF_003201715.1_ASM320171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:51,553] [INFO] Task started: fastANI
[2024-01-24 13:32:51,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f29eca8-648d-4891-90d6-1cbb8576996a/GCF_003201715.1_ASM320171v1_genomic.fna.gz --refList GCF_003201715.1_ASM320171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201715.1_ASM320171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:58,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,694] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:58,695] [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_000613445.1	s__Prevotella shahii	99.8876	1065	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.54	98.05	0.93	0.90	5	conclusive
GCF_000312305.1	s__Prevotella conceptionensis	82.373	715	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.86	95.59	0.91	0.86	4	-
GCF_000378085.1	s__Prevotella loescheii	81.9105	731	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCA_905373605.1	s__Prevotella sp905373605	79.885	476	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127805.1	s__Prevotella sp018127805	78.5371	215	1120	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 13:32:58,697] [INFO] GTDB search result was written to GCF_003201715.1_ASM320171v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:58,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:58,701] [INFO] DFAST_QC result json was written to GCF_003201715.1_ASM320171v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:58,701] [INFO] DFAST_QC completed!
[2024-01-24 13:32:58,701] [INFO] Total running time: 0h1m33s