[2024-01-24 10:47:23,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg2256df5e-601a-4079-8a6f-79d18bc57f95/GCF_003967575.1_ASM396757v1_genomic.fna.gz | prodigal -d GCF_003967575.1_ASM396757v1_genomic.fna/cds.fna -a GCF_003967575.1_ASM396757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:54,745] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:54,746] [INFO] Task started: HMMsearch
[2024-01-24 10:47:54,746] [INFO] Running command: hmmsearch --tblout GCF_003967575.1_ASM396757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/reference_markers.hmm GCF_003967575.1_ASM396757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:55,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:55,139] [INFO] Found 6/6 markers.
[2024-01-24 10:47:55,202] [INFO] Query marker FASTA was written to GCF_003967575.1_ASM396757v1_genomic.fna/markers.fasta
[2024-01-24 10:47:55,203] [INFO] Task started: Blastn
[2024-01-24 10:47:55,203] [INFO] Running command: blastn -query GCF_003967575.1_ASM396757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/reference_markers.fasta -out GCF_003967575.1_ASM396757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:55,790] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:55,796] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:55,797] [INFO] Target genome list was writen to GCF_003967575.1_ASM396757v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:55,827] [INFO] Task started: fastANI
[2024-01-24 10:47:55,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg2256df5e-601a-4079-8a6f-79d18bc57f95/GCF_003967575.1_ASM396757v1_genomic.fna.gz --refList GCF_003967575.1_ASM396757v1_genomic.fna/target_genomes.txt --output GCF_003967575.1_ASM396757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:12,888] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:12,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:12,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:12,899] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:12,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:12,900] [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
Dictyobacter alpinus	strain=Uno16	GCA_003967575.1	2014873	2014873	type	True	100.0	2975	2985	95	conclusive
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	81.7367	1428	2985	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	79.4331	947	2985	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	78.9324	818	2985	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	78.5568	715	2985	95	below_threshold
Ktedonospora formicarum	strain=SOSP1-1	GCA_016587355.1	2778364	2778364	type	True	78.0497	167	2985	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	77.9613	475	2985	95	below_threshold
Thermosporothrix hazakensis	strain=SK20-1	GCA_005402645.1	644383	644383	type	True	76.9281	99	2985	95	below_threshold
Thermosporothrix hazakensis	strain=ATCC BAA-1881	GCA_003253565.1	644383	644383	type	True	76.3411	96	2985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,901] [INFO] DFAST Taxonomy check result was written to GCF_003967575.1_ASM396757v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:12,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:12,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:12,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/checkm_data
[2024-01-24 10:48:12,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:12,991] [INFO] Task started: CheckM
[2024-01-24 10:48:12,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967575.1_ASM396757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967575.1_ASM396757v1_genomic.fna/checkm_input GCF_003967575.1_ASM396757v1_genomic.fna/checkm_result
[2024-01-24 10:49:35,007] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:35,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.19%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:35,042] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:35,042] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:35,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967575.1_ASM396757v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:35,043] [INFO] Task started: Blastn
[2024-01-24 10:49:35,043] [INFO] Running command: blastn -query GCF_003967575.1_ASM396757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4892b09-9a15-4e8e-b7f0-de4abf7df445/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967575.1_ASM396757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:35,795] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:35,798] [INFO] Selected 15 target genomes.
[2024-01-24 10:49:35,799] [INFO] Target genome list was writen to GCF_003967575.1_ASM396757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:35,811] [INFO] Task started: fastANI
[2024-01-24 10:49:35,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg2256df5e-601a-4079-8a6f-79d18bc57f95/GCF_003967575.1_ASM396757v1_genomic.fna.gz --refList GCF_003967575.1_ASM396757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967575.1_ASM396757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:53,982] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:53,998] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:53,998] [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_008974265.1	s__Dictyobacter vulcani	81.7054	1432	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	79.4622	945	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587435.1	s__Dictyobacter sp016587435	78.9062	822	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	78.5601	716	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016587355.1	s__Ktedonobacter sp016587355	78.0471	168	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015099395.1	s__Dictyobacter sp015099395	78.0031	307	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008326305.1	s__Dictyobacter sp008326305	77.9643	476	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208415.1	s__Ktedonosporobacter rubrisoli	77.2955	146	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253565.1	s__Thermosporothrix hazakensis	76.3362	96	2985	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermosporothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:54,000] [INFO] GTDB search result was written to GCF_003967575.1_ASM396757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:54,000] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:54,005] [INFO] DFAST_QC result json was written to GCF_003967575.1_ASM396757v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:54,005] [INFO] DFAST_QC completed!
[2024-01-24 10:49:54,005] [INFO] Total running time: 0h2m30s