[2024-01-24 14:54:49,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,546] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference
[2024-01-24 14:54:50,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,752] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,753] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2c0c052-aa51-4931-9593-e9777d985bc5/GCF_002272945.1_ASM227294v1_genomic.fna.gz | prodigal -d GCF_002272945.1_ASM227294v1_genomic.fna/cds.fna -a GCF_002272945.1_ASM227294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:52,661] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:52,661] [INFO] Task started: HMMsearch
[2024-01-24 14:54:52,661] [INFO] Running command: hmmsearch --tblout GCF_002272945.1_ASM227294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/reference_markers.hmm GCF_002272945.1_ASM227294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:52,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:52,891] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc2c0c052-aa51-4931-9593-e9777d985bc5/GCF_002272945.1_ASM227294v1_genomic.fna.gz]
[2024-01-24 14:54:52,906] [INFO] Query marker FASTA was written to GCF_002272945.1_ASM227294v1_genomic.fna/markers.fasta
[2024-01-24 14:54:52,907] [INFO] Task started: Blastn
[2024-01-24 14:54:52,908] [INFO] Running command: blastn -query GCF_002272945.1_ASM227294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/reference_markers.fasta -out GCF_002272945.1_ASM227294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:53,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:53,458] [INFO] Selected 8 target genomes.
[2024-01-24 14:54:53,459] [INFO] Target genome list was writen to GCF_002272945.1_ASM227294v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:53,522] [INFO] Task started: fastANI
[2024-01-24 14:54:53,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c0c052-aa51-4931-9593-e9777d985bc5/GCF_002272945.1_ASM227294v1_genomic.fna.gz --refList GCF_002272945.1_ASM227294v1_genomic.fna/target_genomes.txt --output GCF_002272945.1_ASM227294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:55,685] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:55,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:55,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:55,692] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:55,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:55,693] [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
Mycoplasmopsis agassizii	strain=PS6	GCA_002272945.1	33922	33922	type	True	100.0	422	422	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:54:55,694] [INFO] DFAST Taxonomy check result was written to GCF_002272945.1_ASM227294v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:55,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:55,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:55,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/checkm_data
[2024-01-24 14:54:55,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:55,713] [INFO] Task started: CheckM
[2024-01-24 14:54:55,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002272945.1_ASM227294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002272945.1_ASM227294v1_genomic.fna/checkm_input GCF_002272945.1_ASM227294v1_genomic.fna/checkm_result
[2024-01-24 14:55:12,144] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:12,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:12,160] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:12,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:12,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002272945.1_ASM227294v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:12,161] [INFO] Task started: Blastn
[2024-01-24 14:55:12,162] [INFO] Running command: blastn -query GCF_002272945.1_ASM227294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd4726ab-900e-42d2-ab1d-5b1f24357da8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002272945.1_ASM227294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:12,833] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:12,837] [INFO] Selected 16 target genomes.
[2024-01-24 14:55:12,837] [INFO] Target genome list was writen to GCF_002272945.1_ASM227294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:12,862] [INFO] Task started: fastANI
[2024-01-24 14:55:12,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c0c052-aa51-4931-9593-e9777d985bc5/GCF_002272945.1_ASM227294v1_genomic.fna.gz --refList GCF_002272945.1_ASM227294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002272945.1_ASM227294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:17,674] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:17,677] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:17,677] [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_900176265.1	s__Mycoplasmopsis_B agassizii	99.9489	406	422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_B	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002276225.1	s__Mycoplasmopsis_B agassizii_A	92.1973	357	422	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:17,678] [INFO] GTDB search result was written to GCF_002272945.1_ASM227294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:17,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:17,681] [INFO] DFAST_QC result json was written to GCF_002272945.1_ASM227294v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:17,681] [INFO] DFAST_QC completed!
[2024-01-24 14:55:17,681] [INFO] Total running time: 0h0m28s