[2024-01-25 19:58:05,718] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:05,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:05,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference
[2024-01-25 19:58:06,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:06,874] [INFO] Task started: Prodigal
[2024-01-25 19:58:06,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg6612c067-1a55-447b-a288-bdc133d220d7/GCF_002950575.1_ASM295057v1_genomic.fna.gz | prodigal -d GCF_002950575.1_ASM295057v1_genomic.fna/cds.fna -a GCF_002950575.1_ASM295057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:12,034] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:12,034] [INFO] Task started: HMMsearch
[2024-01-25 19:58:12,034] [INFO] Running command: hmmsearch --tblout GCF_002950575.1_ASM295057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/reference_markers.hmm GCF_002950575.1_ASM295057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:12,227] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:12,228] [INFO] Found 6/6 markers.
[2024-01-25 19:58:12,244] [INFO] Query marker FASTA was written to GCF_002950575.1_ASM295057v1_genomic.fna/markers.fasta
[2024-01-25 19:58:12,245] [INFO] Task started: Blastn
[2024-01-25 19:58:12,245] [INFO] Running command: blastn -query GCF_002950575.1_ASM295057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/reference_markers.fasta -out GCF_002950575.1_ASM295057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:12,853] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:12,856] [INFO] Selected 22 target genomes.
[2024-01-25 19:58:12,857] [INFO] Target genome list was writen to GCF_002950575.1_ASM295057v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:12,875] [INFO] Task started: fastANI
[2024-01-25 19:58:12,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg6612c067-1a55-447b-a288-bdc133d220d7/GCF_002950575.1_ASM295057v1_genomic.fna.gz --refList GCF_002950575.1_ASM295057v1_genomic.fna/target_genomes.txt --output GCF_002950575.1_ASM295057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:24,746] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:24,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:24,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:24,750] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:24,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:24,750] [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
Pontimonas salivibrio	strain=CL-TW6	GCA_002950575.1	1159327	1159327	type	True	100.0	585	586	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 19:58:24,752] [INFO] DFAST Taxonomy check result was written to GCF_002950575.1_ASM295057v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:24,752] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:24,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:24,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/checkm_data
[2024-01-25 19:58:24,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:24,774] [INFO] Task started: CheckM
[2024-01-25 19:58:24,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002950575.1_ASM295057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002950575.1_ASM295057v1_genomic.fna/checkm_input GCF_002950575.1_ASM295057v1_genomic.fna/checkm_result
[2024-01-25 19:58:45,141] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:45,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:45,156] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:45,156] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:45,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002950575.1_ASM295057v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:45,157] [INFO] Task started: Blastn
[2024-01-25 19:58:45,157] [INFO] Running command: blastn -query GCF_002950575.1_ASM295057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f3ecf0b-5f04-4fad-9eb1-31ed4340509e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002950575.1_ASM295057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:46,077] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:46,080] [INFO] Selected 26 target genomes.
[2024-01-25 19:58:46,080] [INFO] Target genome list was writen to GCF_002950575.1_ASM295057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:46,113] [INFO] Task started: fastANI
[2024-01-25 19:58:46,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg6612c067-1a55-447b-a288-bdc133d220d7/GCF_002950575.1_ASM295057v1_genomic.fna.gz --refList GCF_002950575.1_ASM295057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002950575.1_ASM295057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:59,246] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:59,250] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:59,250] [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_002950575.1	s__Pontimonas salivibrio	100.0	585	586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002172585.1	s__Pontimonas sp002172585	77.6498	96	586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117135.1	s__Pontimonas sp007117135	76.1898	53	586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pontimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:59,252] [INFO] GTDB search result was written to GCF_002950575.1_ASM295057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:59,252] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:59,254] [INFO] DFAST_QC result json was written to GCF_002950575.1_ASM295057v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:59,254] [INFO] DFAST_QC completed!
[2024-01-25 19:58:59,254] [INFO] Total running time: 0h0m54s