[2024-01-24 14:05:01,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:01,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:01,050] [INFO] DQC Reference Directory: /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference
[2024-01-24 14:05:02,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:02,214] [INFO] Task started: Prodigal
[2024-01-24 14:05:02,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg68925518-f8a3-4afa-9a00-84d30c9c913b/GCF_900631685.1_NCTC10126_2_genomic.fna.gz | prodigal -d GCF_900631685.1_NCTC10126_2_genomic.fna/cds.fna -a GCF_900631685.1_NCTC10126_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:04,317] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:04,317] [INFO] Task started: HMMsearch
[2024-01-24 14:05:04,317] [INFO] Running command: hmmsearch --tblout GCF_900631685.1_NCTC10126_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/reference_markers.hmm GCF_900631685.1_NCTC10126_2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:04,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:04,438] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg68925518-f8a3-4afa-9a00-84d30c9c913b/GCF_900631685.1_NCTC10126_2_genomic.fna.gz]
[2024-01-24 14:05:04,454] [INFO] Query marker FASTA was written to GCF_900631685.1_NCTC10126_2_genomic.fna/markers.fasta
[2024-01-24 14:05:04,454] [INFO] Task started: Blastn
[2024-01-24 14:05:04,455] [INFO] Running command: blastn -query GCF_900631685.1_NCTC10126_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/reference_markers.fasta -out GCF_900631685.1_NCTC10126_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:05,000] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:05,004] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:05,004] [INFO] Target genome list was writen to GCF_900631685.1_NCTC10126_2_genomic.fna/target_genomes.txt
[2024-01-24 14:05:05,408] [INFO] Task started: fastANI
[2024-01-24 14:05:05,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg68925518-f8a3-4afa-9a00-84d30c9c913b/GCF_900631685.1_NCTC10126_2_genomic.fna.gz --refList GCF_900631685.1_NCTC10126_2_genomic.fna/target_genomes.txt --output GCF_900631685.1_NCTC10126_2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:08,662] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:08,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:08,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:08,667] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:05:08,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:08,668] [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 caviae	strain=NCTC10126	GCA_900631685.1	55603	55603	type	True	100.0	427	427	95	conclusive
Mycoplasmopsis caviae	strain=G122	GCA_024498215.1	55603	55603	type	True	99.9011	384	427	95	conclusive
Mycoplasmopsis fermentans	strain=PG18	GCA_000209735.1	2115	2115	type	True	81.7562	191	427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:08,669] [INFO] DFAST Taxonomy check result was written to GCF_900631685.1_NCTC10126_2_genomic.fna/tc_result.tsv
[2024-01-24 14:05:08,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:08,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:08,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/checkm_data
[2024-01-24 14:05:08,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:08,686] [INFO] Task started: CheckM
[2024-01-24 14:05:08,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900631685.1_NCTC10126_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900631685.1_NCTC10126_2_genomic.fna/checkm_input GCF_900631685.1_NCTC10126_2_genomic.fna/checkm_result
[2024-01-24 14:05:22,212] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:22,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:22,228] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:22,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:22,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900631685.1_NCTC10126_2_genomic.fna/markers.fasta)
[2024-01-24 14:05:22,229] [INFO] Task started: Blastn
[2024-01-24 14:05:22,229] [INFO] Running command: blastn -query GCF_900631685.1_NCTC10126_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg775a5dd3-c723-49ba-919e-6a6648fe2dc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900631685.1_NCTC10126_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:23,013] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:23,015] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:23,016] [INFO] Target genome list was writen to GCF_900631685.1_NCTC10126_2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:23,050] [INFO] Task started: fastANI
[2024-01-24 14:05:23,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg68925518-f8a3-4afa-9a00-84d30c9c913b/GCF_900631685.1_NCTC10126_2_genomic.fna.gz --refList GCF_900631685.1_NCTC10126_2_genomic.fna/target_genomes_gtdb.txt --output GCF_900631685.1_NCTC10126_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:27,450] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:27,454] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:27,454] [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_900631685.1	s__Mycoplasmopsis caviae	100.0	425	427	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000209735.1	s__Mycoplasmopsis fermentans	81.7562	191	427	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.32	98.97	0.96	0.92	5	-
GCF_017084445.1	s__Mycoplasmopsis sp017084445	78.0594	51	427	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:27,456] [INFO] GTDB search result was written to GCF_900631685.1_NCTC10126_2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:27,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:27,458] [INFO] DFAST_QC result json was written to GCF_900631685.1_NCTC10126_2_genomic.fna/dqc_result.json
[2024-01-24 14:05:27,458] [INFO] DFAST_QC completed!
[2024-01-24 14:05:27,459] [INFO] Total running time: 0h0m26s