[2024-01-24 11:26:11,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,943] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference
[2024-01-24 11:26:13,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,290] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d9da9c5-c90e-483b-b58a-504f7d597a08/GCF_026241165.1_ASM2624116v1_genomic.fna.gz | prodigal -d GCF_026241165.1_ASM2624116v1_genomic.fna/cds.fna -a GCF_026241165.1_ASM2624116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:28,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:28,766] [INFO] Task started: HMMsearch
[2024-01-24 11:26:28,766] [INFO] Running command: hmmsearch --tblout GCF_026241165.1_ASM2624116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/reference_markers.hmm GCF_026241165.1_ASM2624116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:29,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:29,141] [INFO] Found 6/6 markers.
[2024-01-24 11:26:29,180] [INFO] Query marker FASTA was written to GCF_026241165.1_ASM2624116v1_genomic.fna/markers.fasta
[2024-01-24 11:26:29,180] [INFO] Task started: Blastn
[2024-01-24 11:26:29,180] [INFO] Running command: blastn -query GCF_026241165.1_ASM2624116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/reference_markers.fasta -out GCF_026241165.1_ASM2624116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:29,889] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:29,892] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:29,892] [INFO] Target genome list was writen to GCF_026241165.1_ASM2624116v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:29,916] [INFO] Task started: fastANI
[2024-01-24 11:26:29,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d9da9c5-c90e-483b-b58a-504f7d597a08/GCF_026241165.1_ASM2624116v1_genomic.fna.gz --refList GCF_026241165.1_ASM2624116v1_genomic.fna/target_genomes.txt --output GCF_026241165.1_ASM2624116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:44,105] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:44,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:44,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:44,110] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:44,111] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:44,111] [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
Mangrovivirga cuniculi	strain=R1DC9	GCA_005166025.1	2715131	2715131	type	True	84.4433	1142	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:44,116] [INFO] DFAST Taxonomy check result was written to GCF_026241165.1_ASM2624116v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:44,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:44,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:44,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/checkm_data
[2024-01-24 11:26:44,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:44,168] [INFO] Task started: CheckM
[2024-01-24 11:26:44,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026241165.1_ASM2624116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026241165.1_ASM2624116v1_genomic.fna/checkm_input GCF_026241165.1_ASM2624116v1_genomic.fna/checkm_result
[2024-01-24 11:27:32,582] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:32,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:32,605] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:32,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:32,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026241165.1_ASM2624116v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:32,606] [INFO] Task started: Blastn
[2024-01-24 11:27:32,607] [INFO] Running command: blastn -query GCF_026241165.1_ASM2624116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17885bcb-49bd-43bd-9937-007b14e148bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_026241165.1_ASM2624116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:33,525] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:33,530] [INFO] Selected 22 target genomes.
[2024-01-24 11:27:33,530] [INFO] Target genome list was writen to GCF_026241165.1_ASM2624116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:33,565] [INFO] Task started: fastANI
[2024-01-24 11:27:33,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d9da9c5-c90e-483b-b58a-504f7d597a08/GCF_026241165.1_ASM2624116v1_genomic.fna.gz --refList GCF_026241165.1_ASM2624116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026241165.1_ASM2624116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:49,296] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:49,302] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:49,302] [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_005166025.1	s__Fabibacter_A pacificus_A	84.4256	1144	1530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012926615.1	s__Fabibacter_A sp012926615	79.0038	528	1530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,304] [INFO] GTDB search result was written to GCF_026241165.1_ASM2624116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:49,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:49,307] [INFO] DFAST_QC result json was written to GCF_026241165.1_ASM2624116v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:49,307] [INFO] DFAST_QC completed!
[2024-01-24 11:27:49,308] [INFO] Total running time: 0h1m37s