[2024-01-24 13:48:56,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:56,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:56,903] [INFO] DQC Reference Directory: /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference
[2024-01-24 13:48:58,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:58,116] [INFO] Task started: Prodigal
[2024-01-24 13:48:58,116] [INFO] Running command: gunzip -c /var/lib/cwl/stgb08fefbf-c14d-49da-9071-acb79292d689/GCF_004295685.1_ASM429568v1_genomic.fna.gz | prodigal -d GCF_004295685.1_ASM429568v1_genomic.fna/cds.fna -a GCF_004295685.1_ASM429568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:05,555] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:05,555] [INFO] Task started: HMMsearch
[2024-01-24 13:49:05,555] [INFO] Running command: hmmsearch --tblout GCF_004295685.1_ASM429568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/reference_markers.hmm GCF_004295685.1_ASM429568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:05,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:05,810] [INFO] Found 6/6 markers.
[2024-01-24 13:49:05,842] [INFO] Query marker FASTA was written to GCF_004295685.1_ASM429568v1_genomic.fna/markers.fasta
[2024-01-24 13:49:05,843] [INFO] Task started: Blastn
[2024-01-24 13:49:05,843] [INFO] Running command: blastn -query GCF_004295685.1_ASM429568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/reference_markers.fasta -out GCF_004295685.1_ASM429568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:06,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:06,425] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:06,425] [INFO] Target genome list was writen to GCF_004295685.1_ASM429568v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:06,493] [INFO] Task started: fastANI
[2024-01-24 13:49:06,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgb08fefbf-c14d-49da-9071-acb79292d689/GCF_004295685.1_ASM429568v1_genomic.fna.gz --refList GCF_004295685.1_ASM429568v1_genomic.fna/target_genomes.txt --output GCF_004295685.1_ASM429568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:14,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:14,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:14,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:14,263] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:14,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:14,263] [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	100.0	1221	1221	95	conclusive
Fluviispira multicolorata	strain=33A1-SZDP	GCA_009208585.1	2654512	2654512	type	True	80.7489	636	1221	95	below_threshold
Silvanigrella paludirubra	strain=SP-Ram-0.45-NSY-1	GCA_009208775.1	2499159	2499159	type	True	77.6518	282	1221	95	below_threshold
Silvanigrella aquatica	strain=MWH-Nonnen-W8red	GCA_001907975.2	1915309	1915309	type	True	77.5197	257	1221	95	below_threshold
Pigmentibacter ruber	strain=HNSRY-1	GCA_009792895.1	2683196	2683196	type	True	76.9084	202	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:14,265] [INFO] DFAST Taxonomy check result was written to GCF_004295685.1_ASM429568v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:14,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:14,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:14,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/checkm_data
[2024-01-24 13:49:14,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:14,307] [INFO] Task started: CheckM
[2024-01-24 13:49:14,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004295685.1_ASM429568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004295685.1_ASM429568v1_genomic.fna/checkm_input GCF_004295685.1_ASM429568v1_genomic.fna/checkm_result
[2024-01-24 13:49:42,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:42,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:42,903] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:42,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:42,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004295685.1_ASM429568v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:42,904] [INFO] Task started: Blastn
[2024-01-24 13:49:42,905] [INFO] Running command: blastn -query GCF_004295685.1_ASM429568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga09c0284-f4d2-49c5-ad49-370a6bc18b73/dqc_reference/reference_markers_gtdb.fasta -out GCF_004295685.1_ASM429568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,658] [INFO] Selected 9 target genomes.
[2024-01-24 13:49:43,658] [INFO] Target genome list was writen to GCF_004295685.1_ASM429568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:43,694] [INFO] Task started: fastANI
[2024-01-24 13:49:43,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgb08fefbf-c14d-49da-9071-acb79292d689/GCF_004295685.1_ASM429568v1_genomic.fna.gz --refList GCF_004295685.1_ASM429568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004295685.1_ASM429568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:50,102] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,108] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:50,109] [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_004295685.1	s__Silvanigrella sanaruensis	100.0	1221	1221	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	99.33	99.33	0.94	0.94	2	conclusive
GCF_014281055.1	s__Silvanigrella sp014281055	89.0706	998	1221	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208585.1	s__Silvanigrella multicolorata	80.7224	637	1221	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	77.6379	282	1221	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	77.5437	255	1221	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__Silvanigrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792895.1	s__Silvanigrella ruber	76.897	203	1221	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	76.8142	160	1221	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 13:49:50,110] [INFO] GTDB search result was written to GCF_004295685.1_ASM429568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:50,111] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:50,113] [INFO] DFAST_QC result json was written to GCF_004295685.1_ASM429568v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:50,114] [INFO] DFAST_QC completed!
[2024-01-24 13:49:50,114] [INFO] Total running time: 0h0m53s