[2024-01-24 13:25:30,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,055] [INFO] DQC Reference Directory: /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference
[2024-01-24 13:25:31,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,519] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3eeceed-19d3-4d02-820f-062bd6f57644/GCF_000237205.1_ASM23720v1_genomic.fna.gz | prodigal -d GCF_000237205.1_ASM23720v1_genomic.fna/cds.fna -a GCF_000237205.1_ASM23720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:38,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:38,143] [INFO] Task started: HMMsearch
[2024-01-24 13:25:38,143] [INFO] Running command: hmmsearch --tblout GCF_000237205.1_ASM23720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/reference_markers.hmm GCF_000237205.1_ASM23720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:38,463] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:38,464] [INFO] Found 6/6 markers.
[2024-01-24 13:25:38,490] [INFO] Query marker FASTA was written to GCF_000237205.1_ASM23720v1_genomic.fna/markers.fasta
[2024-01-24 13:25:38,490] [INFO] Task started: Blastn
[2024-01-24 13:25:38,491] [INFO] Running command: blastn -query GCF_000237205.1_ASM23720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/reference_markers.fasta -out GCF_000237205.1_ASM23720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:39,078] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:39,082] [INFO] Selected 16 target genomes.
[2024-01-24 13:25:39,082] [INFO] Target genome list was writen to GCF_000237205.1_ASM23720v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:39,096] [INFO] Task started: fastANI
[2024-01-24 13:25:39,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3eeceed-19d3-4d02-820f-062bd6f57644/GCF_000237205.1_ASM23720v1_genomic.fna.gz --refList GCF_000237205.1_ASM23720v1_genomic.fna/target_genomes.txt --output GCF_000237205.1_ASM23720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:48,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:48,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:48,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:48,484] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:48,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:48,484] [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
Simkania negevensis	strain=Z	GCA_000237205.1	83561	83561	type	True	100.0	876	876	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:25:48,485] [INFO] DFAST Taxonomy check result was written to GCF_000237205.1_ASM23720v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:48,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:48,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:48,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/checkm_data
[2024-01-24 13:25:48,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:48,518] [INFO] Task started: CheckM
[2024-01-24 13:25:48,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000237205.1_ASM23720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000237205.1_ASM23720v1_genomic.fna/checkm_input GCF_000237205.1_ASM23720v1_genomic.fna/checkm_result
[2024-01-24 13:26:16,087] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:16,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:16,107] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:16,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:16,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000237205.1_ASM23720v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:16,108] [INFO] Task started: Blastn
[2024-01-24 13:26:16,109] [INFO] Running command: blastn -query GCF_000237205.1_ASM23720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge75cb7a2-16c5-4034-ab5e-b8551ae71f9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000237205.1_ASM23720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:16,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:16,965] [INFO] Selected 19 target genomes.
[2024-01-24 13:26:16,966] [INFO] Target genome list was writen to GCF_000237205.1_ASM23720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:17,017] [INFO] Task started: fastANI
[2024-01-24 13:26:17,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3eeceed-19d3-4d02-820f-062bd6f57644/GCF_000237205.1_ASM23720v1_genomic.fna.gz --refList GCF_000237205.1_ASM23720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000237205.1_ASM23720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:24,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:24,719] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:24,719] [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_000237205.1	s__Simkania negevensis	100.0	876	876	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Simkaniaceae;g__Simkania	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:26:24,723] [INFO] GTDB search result was written to GCF_000237205.1_ASM23720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:24,723] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:24,725] [INFO] DFAST_QC result json was written to GCF_000237205.1_ASM23720v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:24,725] [INFO] DFAST_QC completed!
[2024-01-24 13:26:24,725] [INFO] Total running time: 0h0m55s