[2023-06-29 08:24:17,710] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:24:17,718] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:24:17,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference
[2023-06-29 08:24:20,048] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:24:20,050] [INFO] Task started: Prodigal
[2023-06-29 08:24:20,050] [INFO] Running command: gunzip -c /var/lib/cwl/stga4efec3d-7329-43a4-b98c-e669ea8878ba/GCA_027413355.1_ASM2741335v1_genomic.fna.gz | prodigal -d GCA_027413355.1_ASM2741335v1_genomic.fna/cds.fna -a GCA_027413355.1_ASM2741335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:24:26,827] [INFO] Task succeeded: Prodigal
[2023-06-29 08:24:26,827] [INFO] Task started: HMMsearch
[2023-06-29 08:24:26,828] [INFO] Running command: hmmsearch --tblout GCA_027413355.1_ASM2741335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/reference_markers.hmm GCA_027413355.1_ASM2741335v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:24:27,077] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:24:27,079] [INFO] Found 6/6 markers.
[2023-06-29 08:24:27,106] [INFO] Query marker FASTA was written to GCA_027413355.1_ASM2741335v1_genomic.fna/markers.fasta
[2023-06-29 08:24:27,107] [INFO] Task started: Blastn
[2023-06-29 08:24:27,107] [INFO] Running command: blastn -query GCA_027413355.1_ASM2741335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/reference_markers.fasta -out GCA_027413355.1_ASM2741335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:27,719] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:27,723] [INFO] Selected 15 target genomes.
[2023-06-29 08:24:27,724] [INFO] Target genome list was writen to GCA_027413355.1_ASM2741335v1_genomic.fna/target_genomes.txt
[2023-06-29 08:24:27,731] [INFO] Task started: fastANI
[2023-06-29 08:24:27,731] [INFO] Running command: fastANI --query /var/lib/cwl/stga4efec3d-7329-43a4-b98c-e669ea8878ba/GCA_027413355.1_ASM2741335v1_genomic.fna.gz --refList GCA_027413355.1_ASM2741335v1_genomic.fna/target_genomes.txt --output GCA_027413355.1_ASM2741335v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:24:35,314] [INFO] Task succeeded: fastANI
[2023-06-29 08:24:35,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:24:35,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:24:35,321] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:24:35,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:24:35,322] [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
Ferrimicrobium acidiphilum	strain=T23	GCA_000949255.1	121039	121039	type	True	79.6875	181	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:24:35,324] [INFO] DFAST Taxonomy check result was written to GCA_027413355.1_ASM2741335v1_genomic.fna/tc_result.tsv
[2023-06-29 08:24:35,325] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:24:35,325] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:24:35,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/checkm_data
[2023-06-29 08:24:35,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:24:35,354] [INFO] Task started: CheckM
[2023-06-29 08:24:35,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027413355.1_ASM2741335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027413355.1_ASM2741335v1_genomic.fna/checkm_input GCA_027413355.1_ASM2741335v1_genomic.fna/checkm_result
[2023-06-29 08:25:01,338] [INFO] Task succeeded: CheckM
[2023-06-29 08:25:01,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:25:01,357] [INFO] ===== Completeness check finished =====
[2023-06-29 08:25:01,358] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:25:01,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027413355.1_ASM2741335v1_genomic.fna/markers.fasta)
[2023-06-29 08:25:01,358] [INFO] Task started: Blastn
[2023-06-29 08:25:01,359] [INFO] Running command: blastn -query GCA_027413355.1_ASM2741335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b98145e-63bf-4118-bfdf-5e25be2b9333/dqc_reference/reference_markers_gtdb.fasta -out GCA_027413355.1_ASM2741335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:25:02,234] [INFO] Task succeeded: Blastn
[2023-06-29 08:25:02,238] [INFO] Selected 19 target genomes.
[2023-06-29 08:25:02,239] [INFO] Target genome list was writen to GCA_027413355.1_ASM2741335v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:25:02,273] [INFO] Task started: fastANI
[2023-06-29 08:25:02,273] [INFO] Running command: fastANI --query /var/lib/cwl/stga4efec3d-7329-43a4-b98c-e669ea8878ba/GCA_027413355.1_ASM2741335v1_genomic.fna.gz --refList GCA_027413355.1_ASM2741335v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027413355.1_ASM2741335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:25:11,207] [INFO] Task succeeded: fastANI
[2023-06-29 08:25:11,210] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:25:11,210] [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_000745905.1	s__Ferrimicrobium acidiphilum	79.6803	181	752	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Acidimicrobiaceae;g__Ferrimicrobium	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 08:25:11,212] [INFO] GTDB search result was written to GCA_027413355.1_ASM2741335v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:25:11,213] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:25:11,215] [INFO] DFAST_QC result json was written to GCA_027413355.1_ASM2741335v1_genomic.fna/dqc_result.json
[2023-06-29 08:25:11,215] [INFO] DFAST_QC completed!
[2023-06-29 08:25:11,215] [INFO] Total running time: 0h0m54s