[2024-01-25 19:50:50,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference
[2024-01-25 19:50:51,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,734] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,735] [INFO] Running command: gunzip -c /var/lib/cwl/stgad36ae58-0348-4164-8d70-6a5e3bd5766f/GCF_000026765.1_ASM2676v1_genomic.fna.gz | prodigal -d GCF_000026765.1_ASM2676v1_genomic.fna/cds.fna -a GCF_000026765.1_ASM2676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:53,023] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:53,023] [INFO] Task started: HMMsearch
[2024-01-25 19:50:53,023] [INFO] Running command: hmmsearch --tblout GCF_000026765.1_ASM2676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/reference_markers.hmm GCF_000026765.1_ASM2676v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:53,149] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:53,150] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgad36ae58-0348-4164-8d70-6a5e3bd5766f/GCF_000026765.1_ASM2676v1_genomic.fna.gz]
[2024-01-25 19:50:53,161] [INFO] Query marker FASTA was written to GCF_000026765.1_ASM2676v1_genomic.fna/markers.fasta
[2024-01-25 19:50:53,161] [INFO] Task started: Blastn
[2024-01-25 19:50:53,161] [INFO] Running command: blastn -query GCF_000026765.1_ASM2676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/reference_markers.fasta -out GCF_000026765.1_ASM2676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:53,667] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:53,670] [INFO] Selected 11 target genomes.
[2024-01-25 19:50:53,670] [INFO] Target genome list was writen to GCF_000026765.1_ASM2676v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:53,680] [INFO] Task started: fastANI
[2024-01-25 19:50:53,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgad36ae58-0348-4164-8d70-6a5e3bd5766f/GCF_000026765.1_ASM2676v1_genomic.fna.gz --refList GCF_000026765.1_ASM2676v1_genomic.fna/target_genomes.txt --output GCF_000026765.1_ASM2676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:56,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:56,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:56,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:56,281] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:56,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:56,281] [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
Mesomycoplasma conjunctivae	strain=HRC/581T	GCA_000026765.1	45361	45361	type	True	100.0	279	282	95	conclusive
Mesomycoplasma bovoculi	strain=M165/69	GCA_000524555.1	45362	45362	type	True	78.3831	67	282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:56,282] [INFO] DFAST Taxonomy check result was written to GCF_000026765.1_ASM2676v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:56,290] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:56,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:56,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/checkm_data
[2024-01-25 19:50:56,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:56,302] [INFO] Task started: CheckM
[2024-01-25 19:50:56,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000026765.1_ASM2676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000026765.1_ASM2676v1_genomic.fna/checkm_input GCF_000026765.1_ASM2676v1_genomic.fna/checkm_result
[2024-01-25 19:51:07,235] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:07,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:07,249] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:07,249] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:07,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000026765.1_ASM2676v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:07,250] [INFO] Task started: Blastn
[2024-01-25 19:51:07,250] [INFO] Running command: blastn -query GCF_000026765.1_ASM2676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a3c456d-4f6f-4bd1-bfa4-9a6e95e6a06e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000026765.1_ASM2676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:07,913] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:07,916] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:07,916] [INFO] Target genome list was writen to GCF_000026765.1_ASM2676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:07,927] [INFO] Task started: fastANI
[2024-01-25 19:51:07,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgad36ae58-0348-4164-8d70-6a5e3bd5766f/GCF_000026765.1_ASM2676v1_genomic.fna.gz --refList GCF_000026765.1_ASM2676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000026765.1_ASM2676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:11,962] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:11,965] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:11,965] [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_000026765.1	s__Mesomycoplasma conjunctivae	100.0	279	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000524555.1	s__Mesomycoplasma bovoculi	78.3831	67	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:11,966] [INFO] GTDB search result was written to GCF_000026765.1_ASM2676v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:11,967] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:11,968] [INFO] DFAST_QC result json was written to GCF_000026765.1_ASM2676v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:11,969] [INFO] DFAST_QC completed!
[2024-01-25 19:51:11,969] [INFO] Total running time: 0h0m21s