[2024-01-24 13:28:11,796] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference
[2024-01-24 13:28:13,076] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:13,077] [INFO] Task started: Prodigal
[2024-01-24 13:28:13,077] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbba035a-9f0e-4f47-833b-fd62f4f67929/GCF_009208585.1_ASM920858v1_genomic.fna.gz | prodigal -d GCF_009208585.1_ASM920858v1_genomic.fna/cds.fna -a GCF_009208585.1_ASM920858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:19,548] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:19,548] [INFO] Task started: HMMsearch
[2024-01-24 13:28:19,549] [INFO] Running command: hmmsearch --tblout GCF_009208585.1_ASM920858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/reference_markers.hmm GCF_009208585.1_ASM920858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:19,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:19,820] [INFO] Found 6/6 markers.
[2024-01-24 13:28:19,861] [INFO] Query marker FASTA was written to GCF_009208585.1_ASM920858v1_genomic.fna/markers.fasta
[2024-01-24 13:28:19,862] [INFO] Task started: Blastn
[2024-01-24 13:28:19,862] [INFO] Running command: blastn -query GCF_009208585.1_ASM920858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/reference_markers.fasta -out GCF_009208585.1_ASM920858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:20,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:20,425] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:20,425] [INFO] Target genome list was writen to GCF_009208585.1_ASM920858v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:20,435] [INFO] Task started: fastANI
[2024-01-24 13:28:20,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbba035a-9f0e-4f47-833b-fd62f4f67929/GCF_009208585.1_ASM920858v1_genomic.fna.gz --refList GCF_009208585.1_ASM920858v1_genomic.fna/target_genomes.txt --output GCF_009208585.1_ASM920858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:26,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:26,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:26,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:26,914] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:26,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:26,915] [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
Fluviispira multicolorata	strain=33A1-SZDP	GCA_009208585.1	2654512	2654512	type	True	100.0	1121	1121	95	conclusive
Fluviispira sanaruensis	strain=RF1110005	GCA_004295685.1	2493639	2493639	type	True	80.6247	653	1121	95	below_threshold
Silvanigrella aquatica	strain=MWH-Nonnen-W8red	GCA_001907975.2	1915309	1915309	type	True	77.5141	271	1121	95	below_threshold
Silvanigrella paludirubra	strain=SP-Ram-0.45-NSY-1	GCA_009208775.1	2499159	2499159	type	True	77.4608	335	1121	95	below_threshold
Pigmentibacter ruber	strain=HNSRY-1	GCA_009792895.1	2683196	2683196	type	True	76.6925	241	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:26,917] [INFO] DFAST Taxonomy check result was written to GCF_009208585.1_ASM920858v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:26,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:26,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:26,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/checkm_data
[2024-01-24 13:28:26,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:26,954] [INFO] Task started: CheckM
[2024-01-24 13:28:26,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009208585.1_ASM920858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009208585.1_ASM920858v1_genomic.fna/checkm_input GCF_009208585.1_ASM920858v1_genomic.fna/checkm_result
[2024-01-24 13:28:52,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:52,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:52,785] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:52,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:52,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009208585.1_ASM920858v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:52,786] [INFO] Task started: Blastn
[2024-01-24 13:28:52,786] [INFO] Running command: blastn -query GCF_009208585.1_ASM920858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c379c28-5b2a-49be-b5bb-05b70ae9b222/dqc_reference/reference_markers_gtdb.fasta -out GCF_009208585.1_ASM920858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:53,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:53,542] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:53,542] [INFO] Target genome list was writen to GCF_009208585.1_ASM920858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:53,636] [INFO] Task started: fastANI
[2024-01-24 13:28:53,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbba035a-9f0e-4f47-833b-fd62f4f67929/GCF_009208585.1_ASM920858v1_genomic.fna.gz --refList GCF_009208585.1_ASM920858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009208585.1_ASM920858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:00,756] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:00,768] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:00,768] [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_009208585.1	s__Silvanigrella multicolorata	100.0	1121	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004295685.1	s__Silvanigrella sanaruensis	80.6344	652	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	99.33	99.33	0.94	0.94	2	-
GCF_014281055.1	s__Silvanigrella sp014281055	80.5256	634	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907975.1	s__Silvanigrella aquatica	77.5899	271	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208775.1	s__Silvanigrella paludirubra	77.4699	334	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003339605.1	s__Silvanigrella cienkowskii	76.7739	183	1121	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,771] [INFO] GTDB search result was written to GCF_009208585.1_ASM920858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:00,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:00,774] [INFO] DFAST_QC result json was written to GCF_009208585.1_ASM920858v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:00,774] [INFO] DFAST_QC completed!
[2024-01-24 13:29:00,774] [INFO] Total running time: 0h0m49s