[2024-01-25 17:47:20,390] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:20,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:20,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference
[2024-01-25 17:47:21,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:21,567] [INFO] Task started: Prodigal
[2024-01-25 17:47:21,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg8790ac1b-aeb9-40f5-a2ed-fa74f8012978/GCF_000143945.1_ASM14394v1_genomic.fna.gz | prodigal -d GCF_000143945.1_ASM14394v1_genomic.fna/cds.fna -a GCF_000143945.1_ASM14394v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:24,451] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:24,451] [INFO] Task started: HMMsearch
[2024-01-25 17:47:24,452] [INFO] Running command: hmmsearch --tblout GCF_000143945.1_ASM14394v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/reference_markers.hmm GCF_000143945.1_ASM14394v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:24,590] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:24,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8790ac1b-aeb9-40f5-a2ed-fa74f8012978/GCF_000143945.1_ASM14394v1_genomic.fna.gz]
[2024-01-25 17:47:24,607] [INFO] Query marker FASTA was written to GCF_000143945.1_ASM14394v1_genomic.fna/markers.fasta
[2024-01-25 17:47:24,608] [INFO] Task started: Blastn
[2024-01-25 17:47:24,608] [INFO] Running command: blastn -query GCF_000143945.1_ASM14394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/reference_markers.fasta -out GCF_000143945.1_ASM14394v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:25,144] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:25,150] [INFO] Selected 7 target genomes.
[2024-01-25 17:47:25,150] [INFO] Target genome list was writen to GCF_000143945.1_ASM14394v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:25,154] [INFO] Task started: fastANI
[2024-01-25 17:47:25,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg8790ac1b-aeb9-40f5-a2ed-fa74f8012978/GCF_000143945.1_ASM14394v1_genomic.fna.gz --refList GCF_000143945.1_ASM14394v1_genomic.fna/target_genomes.txt --output GCF_000143945.1_ASM14394v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:28,438] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:28,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:28,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:28,443] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:47:28,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:28,444] [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
Mycoplasmoides pneumoniae	strain=NCTC10119	GCA_900660465.1	2104	2104	type	True	99.9874	268	270	95	conclusive
Mycoplasmoides pneumoniae	strain=FH	GCA_001272835.1	2104	2104	type	True	99.9756	269	270	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:47:28,445] [INFO] DFAST Taxonomy check result was written to GCF_000143945.1_ASM14394v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:28,445] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:28,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:28,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/checkm_data
[2024-01-25 17:47:28,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:28,459] [INFO] Task started: CheckM
[2024-01-25 17:47:28,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000143945.1_ASM14394v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000143945.1_ASM14394v1_genomic.fna/checkm_input GCF_000143945.1_ASM14394v1_genomic.fna/checkm_result
[2024-01-25 17:47:43,153] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:43,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:43,173] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:43,173] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:43,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000143945.1_ASM14394v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:43,174] [INFO] Task started: Blastn
[2024-01-25 17:47:43,174] [INFO] Running command: blastn -query GCF_000143945.1_ASM14394v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec76580f-0058-4d28-b9bd-eb864c4c2cd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000143945.1_ASM14394v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:43,887] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:43,891] [INFO] Selected 10 target genomes.
[2024-01-25 17:47:43,891] [INFO] Target genome list was writen to GCF_000143945.1_ASM14394v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:43,899] [INFO] Task started: fastANI
[2024-01-25 17:47:43,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg8790ac1b-aeb9-40f5-a2ed-fa74f8012978/GCF_000143945.1_ASM14394v1_genomic.fna.gz --refList GCF_000143945.1_ASM14394v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000143945.1_ASM14394v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:47,960] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:47,962] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:47,962] [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_001272835.1	s__Mycoplasmoides pneumoniae	99.9756	269	270	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmoidaceae;g__Mycoplasmoides	95.0	99.86	99.73	0.99	0.98	185	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:47:47,964] [INFO] GTDB search result was written to GCF_000143945.1_ASM14394v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:47,964] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:47,966] [INFO] DFAST_QC result json was written to GCF_000143945.1_ASM14394v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:47,966] [INFO] DFAST_QC completed!
[2024-01-25 17:47:47,966] [INFO] Total running time: 0h0m28s