[2024-01-24 13:18:26,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference
[2024-01-24 13:18:27,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,506] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgacbe0f45-abf7-46a4-9ce6-4e987e316d6f/GCF_014281055.1_ASM1428105v1_genomic.fna.gz | prodigal -d GCF_014281055.1_ASM1428105v1_genomic.fna/cds.fna -a GCF_014281055.1_ASM1428105v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:35,256] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:35,257] [INFO] Task started: HMMsearch
[2024-01-24 13:18:35,257] [INFO] Running command: hmmsearch --tblout GCF_014281055.1_ASM1428105v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/reference_markers.hmm GCF_014281055.1_ASM1428105v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:35,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:35,541] [INFO] Found 6/6 markers.
[2024-01-24 13:18:35,579] [INFO] Query marker FASTA was written to GCF_014281055.1_ASM1428105v1_genomic.fna/markers.fasta
[2024-01-24 13:18:35,579] [INFO] Task started: Blastn
[2024-01-24 13:18:35,579] [INFO] Running command: blastn -query GCF_014281055.1_ASM1428105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/reference_markers.fasta -out GCF_014281055.1_ASM1428105v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:36,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:36,150] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:36,151] [INFO] Target genome list was writen to GCF_014281055.1_ASM1428105v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:36,164] [INFO] Task started: fastANI
[2024-01-24 13:18:36,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbe0f45-abf7-46a4-9ce6-4e987e316d6f/GCF_014281055.1_ASM1428105v1_genomic.fna.gz --refList GCF_014281055.1_ASM1428105v1_genomic.fna/target_genomes.txt --output GCF_014281055.1_ASM1428105v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:44,938] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:44,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:44,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:44,947] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:44,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:44,948] [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 sanaruensis	strain=RF1110005	GCA_004295685.1	2493639	2493639	type	True	89.2137	995	1197	95	below_threshold
Fluviispira multicolorata	strain=33A1-SZDP	GCA_009208585.1	2654512	2654512	type	True	80.6337	635	1197	95	below_threshold
Silvanigrella paludirubra	strain=SP-Ram-0.45-NSY-1	GCA_009208775.1	2499159	2499159	type	True	77.3582	291	1197	95	below_threshold
Silvanigrella aquatica	strain=MWH-Nonnen-W8red	GCA_001907975.2	1915309	1915309	type	True	77.2332	253	1197	95	below_threshold
Pigmentibacter ruber	strain=HNSRY-1	GCA_009792895.1	2683196	2683196	type	True	76.683	217	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,949] [INFO] DFAST Taxonomy check result was written to GCF_014281055.1_ASM1428105v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:44,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:44,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:44,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/checkm_data
[2024-01-24 13:18:44,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:44,990] [INFO] Task started: CheckM
[2024-01-24 13:18:44,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014281055.1_ASM1428105v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014281055.1_ASM1428105v1_genomic.fna/checkm_input GCF_014281055.1_ASM1428105v1_genomic.fna/checkm_result
[2024-01-24 13:19:14,528] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:14,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,544] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:14,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:14,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014281055.1_ASM1428105v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:14,546] [INFO] Task started: Blastn
[2024-01-24 13:19:14,546] [INFO] Running command: blastn -query GCF_014281055.1_ASM1428105v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b2f1da5-8d90-4fd3-8784-086f8627de17/dqc_reference/reference_markers_gtdb.fasta -out GCF_014281055.1_ASM1428105v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:15,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:15,364] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:15,364] [INFO] Target genome list was writen to GCF_014281055.1_ASM1428105v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:15,375] [INFO] Task started: fastANI
[2024-01-24 13:19:15,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbe0f45-abf7-46a4-9ce6-4e987e316d6f/GCF_014281055.1_ASM1428105v1_genomic.fna.gz --refList GCF_014281055.1_ASM1428105v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014281055.1_ASM1428105v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:22,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:22,072] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:22,072] [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_014281055.1	s__Silvanigrella sp014281055	100.0	1195	1197	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	89.2137	995	1197	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	99.33	99.33	0.94	0.94	2	-
GCF_009208585.1	s__Silvanigrella multicolorata	80.6241	636	1197	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	77.3472	293	1197	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	77.2532	251	1197	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	77.0103	149	1197	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 13:19:22,074] [INFO] GTDB search result was written to GCF_014281055.1_ASM1428105v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:22,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:22,077] [INFO] DFAST_QC result json was written to GCF_014281055.1_ASM1428105v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:22,077] [INFO] DFAST_QC completed!
[2024-01-24 13:19:22,077] [INFO] Total running time: 0h0m56s