[2024-01-24 14:05:30,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:30,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:30,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference
[2024-01-24 14:05:31,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:31,641] [INFO] Task started: Prodigal
[2024-01-24 14:05:31,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8e6a954-1efe-4bb5-91bb-37591cac9d2e/GCF_900475235.1_43116_D01_genomic.fna.gz | prodigal -d GCF_900475235.1_43116_D01_genomic.fna/cds.fna -a GCF_900475235.1_43116_D01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:32,914] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:32,914] [INFO] Task started: HMMsearch
[2024-01-24 14:05:32,915] [INFO] Running command: hmmsearch --tblout GCF_900475235.1_43116_D01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/reference_markers.hmm GCF_900475235.1_43116_D01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:33,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:33,098] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc8e6a954-1efe-4bb5-91bb-37591cac9d2e/GCF_900475235.1_43116_D01_genomic.fna.gz]
[2024-01-24 14:05:33,115] [INFO] Query marker FASTA was written to GCF_900475235.1_43116_D01_genomic.fna/markers.fasta
[2024-01-24 14:05:33,115] [INFO] Task started: Blastn
[2024-01-24 14:05:33,115] [INFO] Running command: blastn -query GCF_900475235.1_43116_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/reference_markers.fasta -out GCF_900475235.1_43116_D01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:33,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:33,651] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:33,651] [INFO] Target genome list was writen to GCF_900475235.1_43116_D01_genomic.fna/target_genomes.txt
[2024-01-24 14:05:33,666] [INFO] Task started: fastANI
[2024-01-24 14:05:33,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e6a954-1efe-4bb5-91bb-37591cac9d2e/GCF_900475235.1_43116_D01_genomic.fna.gz --refList GCF_900475235.1_43116_D01_genomic.fna/target_genomes.txt --output GCF_900475235.1_43116_D01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:36,171] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:36,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:36,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:36,180] [INFO] Found 3 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:05:36,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:36,180] [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 synoviae	strain=NCTC10124	GCA_900475235.1	2109	2109	type	True	100.0	282	282	95	conclusive
Mycoplasmopsis synoviae	strain=WVU1853	GCA_000969765.1	2109	2109	type	True	99.9591	276	282	95	conclusive
Mycoplasmopsis synoviae	strain=WVU 1853	GCA_000385095.1	2109	2109	type	True	99.7647	221	282	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:05:36,182] [INFO] DFAST Taxonomy check result was written to GCF_900475235.1_43116_D01_genomic.fna/tc_result.tsv
[2024-01-24 14:05:36,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:36,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:36,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/checkm_data
[2024-01-24 14:05:36,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:36,197] [INFO] Task started: CheckM
[2024-01-24 14:05:36,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475235.1_43116_D01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475235.1_43116_D01_genomic.fna/checkm_input GCF_900475235.1_43116_D01_genomic.fna/checkm_result
[2024-01-24 14:05:48,881] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:48,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:48,917] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:48,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:48,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475235.1_43116_D01_genomic.fna/markers.fasta)
[2024-01-24 14:05:48,919] [INFO] Task started: Blastn
[2024-01-24 14:05:48,919] [INFO] Running command: blastn -query GCF_900475235.1_43116_D01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70e3b3b-0642-4ce4-bd1d-29fe25544ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475235.1_43116_D01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,603] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,606] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:49,606] [INFO] Target genome list was writen to GCF_900475235.1_43116_D01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:49,616] [INFO] Task started: fastANI
[2024-01-24 14:05:49,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e6a954-1efe-4bb5-91bb-37591cac9d2e/GCF_900475235.1_43116_D01_genomic.fna.gz --refList GCF_900475235.1_43116_D01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475235.1_43116_D01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:54,518] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:54,521] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:54,521] [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_000969765.1	s__Mycoplasmopsis_A synoviae	99.9591	276	282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.16	98.68	0.98	0.96	11	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:05:54,524] [INFO] GTDB search result was written to GCF_900475235.1_43116_D01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:54,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:54,526] [INFO] DFAST_QC result json was written to GCF_900475235.1_43116_D01_genomic.fna/dqc_result.json
[2024-01-24 14:05:54,526] [INFO] DFAST_QC completed!
[2024-01-24 14:05:54,527] [INFO] Total running time: 0h0m24s