[2024-01-24 13:25:28,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:28,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:28,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference
[2024-01-24 13:25:29,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:29,694] [INFO] Task started: Prodigal
[2024-01-24 13:25:29,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgd659db88-478f-474b-8242-1f120b24d471/GCF_007747445.1_ASM774744v1_genomic.fna.gz | prodigal -d GCF_007747445.1_ASM774744v1_genomic.fna/cds.fna -a GCF_007747445.1_ASM774744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,225] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,226] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,226] [INFO] Running command: hmmsearch --tblout GCF_007747445.1_ASM774744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/reference_markers.hmm GCF_007747445.1_ASM774744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,595] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,635] [INFO] Query marker FASTA was written to GCF_007747445.1_ASM774744v1_genomic.fna/markers.fasta
[2024-01-24 13:25:42,636] [INFO] Task started: Blastn
[2024-01-24 13:25:42,636] [INFO] Running command: blastn -query GCF_007747445.1_ASM774744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/reference_markers.fasta -out GCF_007747445.1_ASM774744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,279] [INFO] Selected 33 target genomes.
[2024-01-24 13:25:43,279] [INFO] Target genome list was writen to GCF_007747445.1_ASM774744v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,308] [INFO] Task started: fastANI
[2024-01-24 13:25:43,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgd659db88-478f-474b-8242-1f120b24d471/GCF_007747445.1_ASM774744v1_genomic.fna.gz --refList GCF_007747445.1_ASM774744v1_genomic.fna/target_genomes.txt --output GCF_007747445.1_ASM774744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:07,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:07,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:07,156] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:07,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:07,157] [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
Poriferisphaera corsica	strain=KS4	GCA_007747445.1	2528020	2528020	type	True	100.0	1430	1430	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,159] [INFO] DFAST Taxonomy check result was written to GCF_007747445.1_ASM774744v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:07,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:07,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:07,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/checkm_data
[2024-01-24 13:26:07,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:07,203] [INFO] Task started: CheckM
[2024-01-24 13:26:07,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007747445.1_ASM774744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007747445.1_ASM774744v1_genomic.fna/checkm_input GCF_007747445.1_ASM774744v1_genomic.fna/checkm_result
[2024-01-24 13:26:47,668] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:47,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:47,689] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:47,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:47,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007747445.1_ASM774744v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:47,690] [INFO] Task started: Blastn
[2024-01-24 13:26:47,690] [INFO] Running command: blastn -query GCF_007747445.1_ASM774744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd823aacb-1477-42f7-969c-ad95779abdf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_007747445.1_ASM774744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:48,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:48,484] [INFO] Selected 29 target genomes.
[2024-01-24 13:26:48,484] [INFO] Target genome list was writen to GCF_007747445.1_ASM774744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:48,542] [INFO] Task started: fastANI
[2024-01-24 13:26:48,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgd659db88-478f-474b-8242-1f120b24d471/GCF_007747445.1_ASM774744v1_genomic.fna.gz --refList GCF_007747445.1_ASM774744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007747445.1_ASM774744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:06,153] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:06,159] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:06,160] [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_007747445.1	s__Poriferisphaera corsica	100.0	1430	1430	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Poriferisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016350165.1	s__Poriferisphaera sp016350165	79.6945	507	1430	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Poriferisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:06,161] [INFO] GTDB search result was written to GCF_007747445.1_ASM774744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:06,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:06,164] [INFO] DFAST_QC result json was written to GCF_007747445.1_ASM774744v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:06,164] [INFO] DFAST_QC completed!
[2024-01-24 13:27:06,164] [INFO] Total running time: 0h1m38s