[2023-06-05 08:48:48,252] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:48:48,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:48:48,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference
[2023-06-05 08:48:50,954] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:48:50,956] [INFO] Task started: Prodigal
[2023-06-05 08:48:50,956] [INFO] Running command: gunzip -c /var/lib/cwl/stge5305e2c-fb22-439b-b2bc-7fdc0336110f/GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna.gz | prodigal -d GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/cds.fna -a GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:48:52,984] [INFO] Task succeeded: Prodigal
[2023-06-05 08:48:52,984] [INFO] Task started: HMMsearch
[2023-06-05 08:48:52,984] [INFO] Running command: hmmsearch --tblout GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/reference_markers.hmm GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:48:53,224] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:48:53,225] [INFO] Found 6/6 markers.
[2023-06-05 08:48:53,247] [INFO] Query marker FASTA was written to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/markers.fasta
[2023-06-05 08:48:53,247] [INFO] Task started: Blastn
[2023-06-05 08:48:53,247] [INFO] Running command: blastn -query GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/reference_markers.fasta -out GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:48:55,348] [INFO] Task succeeded: Blastn
[2023-06-05 08:48:55,352] [INFO] Selected 22 target genomes.
[2023-06-05 08:48:55,353] [INFO] Target genome list was writen to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/target_genomes.txt
[2023-06-05 08:48:55,385] [INFO] Task started: fastANI
[2023-06-05 08:48:55,385] [INFO] Running command: fastANI --query /var/lib/cwl/stge5305e2c-fb22-439b-b2bc-7fdc0336110f/GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna.gz --refList GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/target_genomes.txt --output GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:49:04,889] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:04,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:49:04,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:49:04,900] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:49:04,901] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:49:04,901] [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
--------------------------------------------------------------------------------
[2023-06-05 08:49:04,905] [INFO] DFAST Taxonomy check result was written to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/tc_result.tsv
[2023-06-05 08:49:04,908] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:49:04,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:49:04,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/checkm_data
[2023-06-05 08:49:04,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:49:04,970] [INFO] Task started: CheckM
[2023-06-05 08:49:04,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/checkm_input GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/checkm_result
[2023-06-05 08:49:21,721] [INFO] Task succeeded: CheckM
[2023-06-05 08:49:21,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:49:21,750] [INFO] ===== Completeness check finished =====
[2023-06-05 08:49:21,752] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:49:21,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/markers.fasta)
[2023-06-05 08:49:21,754] [INFO] Task started: Blastn
[2023-06-05 08:49:21,754] [INFO] Running command: blastn -query GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a27cdcd-c6f3-40b0-a36d-f0026892ae26/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:22,524] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:22,531] [INFO] Selected 11 target genomes.
[2023-06-05 08:49:22,532] [INFO] Target genome list was writen to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:49:22,591] [INFO] Task started: fastANI
[2023-06-05 08:49:22,592] [INFO] Running command: fastANI --query /var/lib/cwl/stge5305e2c-fb22-439b-b2bc-7fdc0336110f/GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna.gz --refList GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/target_genomes_gtdb.txt --output GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:49:25,354] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:25,361] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:49:25,362] [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
GCA_900318975.1	s__UBA1188 sp900318975	99.9999	255	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_017541975.1	s__UBA1188 sp017541975	84.4667	143	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017960565.1	s__UBA1188 sp017960565	80.9699	142	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310135.1	s__UBA1188 sp002310135	78.3095	56	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Izemoplasmatales;f__UBA1188;g__UBA1188	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:49:25,373] [INFO] GTDB search result was written to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/result_gtdb.tsv
[2023-06-05 08:49:25,374] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:49:25,378] [INFO] DFAST_QC result json was written to GCA_902759855.1_Rumen_uncultured_genome_RUG10507_genomic.fna/dqc_result.json
[2023-06-05 08:49:25,378] [INFO] DFAST_QC completed!
[2023-06-05 08:49:25,378] [INFO] Total running time: 0h0m37s