[2024-01-25 20:03:20,378] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:20,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:20,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference
[2024-01-25 20:03:21,524] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:21,525] [INFO] Task started: Prodigal
[2024-01-25 20:03:21,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ca8c6bb-6a0e-4414-873e-727534f353b6/GCF_009208775.1_ASM920877v1_genomic.fna.gz | prodigal -d GCF_009208775.1_ASM920877v1_genomic.fna/cds.fna -a GCF_009208775.1_ASM920877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:27,336] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:27,336] [INFO] Task started: HMMsearch
[2024-01-25 20:03:27,336] [INFO] Running command: hmmsearch --tblout GCF_009208775.1_ASM920877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/reference_markers.hmm GCF_009208775.1_ASM920877v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:27,546] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:27,547] [INFO] Found 6/6 markers.
[2024-01-25 20:03:27,576] [INFO] Query marker FASTA was written to GCF_009208775.1_ASM920877v1_genomic.fna/markers.fasta
[2024-01-25 20:03:27,576] [INFO] Task started: Blastn
[2024-01-25 20:03:27,576] [INFO] Running command: blastn -query GCF_009208775.1_ASM920877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/reference_markers.fasta -out GCF_009208775.1_ASM920877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:28,094] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:28,097] [INFO] Selected 14 target genomes.
[2024-01-25 20:03:28,097] [INFO] Target genome list was writen to GCF_009208775.1_ASM920877v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:28,106] [INFO] Task started: fastANI
[2024-01-25 20:03:28,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca8c6bb-6a0e-4414-873e-727534f353b6/GCF_009208775.1_ASM920877v1_genomic.fna.gz --refList GCF_009208775.1_ASM920877v1_genomic.fna/target_genomes.txt --output GCF_009208775.1_ASM920877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:37,327] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:37,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:37,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:37,332] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:37,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:37,333] [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
Silvanigrella paludirubra	strain=SP-Ram-0.45-NSY-1	GCA_009208775.1	2499159	2499159	type	True	100.0	1301	1303	95	conclusive
Silvanigrella aquatica	strain=MWH-Nonnen-W8red	GCA_001907975.2	1915309	1915309	type	True	78.907	486	1303	95	below_threshold
Pigmentibacter ruber	strain=HNSRY-1	GCA_009792895.1	2683196	2683196	type	True	78.035	444	1303	95	below_threshold
Fluviispira sanaruensis	strain=RF1110005	GCA_004295685.1	2493639	2493639	type	True	77.549	268	1303	95	below_threshold
Fluviispira multicolorata	strain=33A1-SZDP	GCA_009208585.1	2654512	2654512	type	True	77.4602	323	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:37,334] [INFO] DFAST Taxonomy check result was written to GCF_009208775.1_ASM920877v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:37,335] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:37,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:37,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/checkm_data
[2024-01-25 20:03:37,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:37,375] [INFO] Task started: CheckM
[2024-01-25 20:03:37,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009208775.1_ASM920877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009208775.1_ASM920877v1_genomic.fna/checkm_input GCF_009208775.1_ASM920877v1_genomic.fna/checkm_result
[2024-01-25 20:04:00,378] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:00,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:00,392] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:00,393] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:00,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009208775.1_ASM920877v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:00,393] [INFO] Task started: Blastn
[2024-01-25 20:04:00,393] [INFO] Running command: blastn -query GCF_009208775.1_ASM920877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d998a37-1370-41f3-b385-3938fd7f993a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009208775.1_ASM920877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:01,180] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:01,183] [INFO] Selected 16 target genomes.
[2024-01-25 20:04:01,184] [INFO] Target genome list was writen to GCF_009208775.1_ASM920877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:01,206] [INFO] Task started: fastANI
[2024-01-25 20:04:01,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca8c6bb-6a0e-4414-873e-727534f353b6/GCF_009208775.1_ASM920877v1_genomic.fna.gz --refList GCF_009208775.1_ASM920877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009208775.1_ASM920877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:13,035] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:13,040] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:13,040] [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_009208775.1	s__Silvanigrella paludirubra	100.0	1301	1303	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_001907975.1	s__Silvanigrella aquatica	78.9124	485	1303	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295685.1	s__Silvanigrella sanaruensis	77.549	268	1303	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	77.5027	325	1303	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281055.1	s__Silvanigrella sp014281055	77.4538	275	1303	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	77.1227	263	1303	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:13,041] [INFO] GTDB search result was written to GCF_009208775.1_ASM920877v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:13,042] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:13,044] [INFO] DFAST_QC result json was written to GCF_009208775.1_ASM920877v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:13,044] [INFO] DFAST_QC completed!
[2024-01-25 20:04:13,044] [INFO] Total running time: 0h0m53s