[2023-06-04 19:18:30,104] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:18:30,119] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:18:30,119] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference
[2023-06-04 19:18:31,389] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:18:31,390] [INFO] Task started: Prodigal
[2023-06-04 19:18:31,390] [INFO] Running command: gunzip -c /var/lib/cwl/stg93c89d53-db01-493b-92a0-84239b1d386d/GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna.gz | prodigal -d GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/cds.fna -a GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:18:34,421] [INFO] Task succeeded: Prodigal
[2023-06-04 19:18:34,421] [INFO] Task started: HMMsearch
[2023-06-04 19:18:34,421] [INFO] Running command: hmmsearch --tblout GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/reference_markers.hmm GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:18:34,613] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:18:34,614] [INFO] Found 6/6 markers.
[2023-06-04 19:18:34,630] [INFO] Query marker FASTA was written to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/markers.fasta
[2023-06-04 19:18:34,631] [INFO] Task started: Blastn
[2023-06-04 19:18:34,631] [INFO] Running command: blastn -query GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/reference_markers.fasta -out GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:18:35,221] [INFO] Task succeeded: Blastn
[2023-06-04 19:18:35,225] [INFO] Selected 26 target genomes.
[2023-06-04 19:18:35,225] [INFO] Target genome list was writen to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/target_genomes.txt
[2023-06-04 19:18:35,288] [INFO] Task started: fastANI
[2023-06-04 19:18:35,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg93c89d53-db01-493b-92a0-84239b1d386d/GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna.gz --refList GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/target_genomes.txt --output GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:18:47,913] [INFO] Task succeeded: fastANI
[2023-06-04 19:18:47,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:18:47,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:18:47,915] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:18:47,915] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:18:47,915] [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
--------------------------------------------------------------------------------
[2023-06-04 19:18:47,917] [INFO] DFAST Taxonomy check result was written to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/tc_result.tsv
[2023-06-04 19:18:47,917] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:18:47,918] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:18:47,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/checkm_data
[2023-06-04 19:18:47,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:18:47,945] [INFO] Task started: CheckM
[2023-06-04 19:18:47,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/checkm_input GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/checkm_result
[2023-06-04 19:19:03,863] [INFO] Task succeeded: CheckM
[2023-06-04 19:19:03,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:19:03,880] [INFO] ===== Completeness check finished =====
[2023-06-04 19:19:03,880] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:19:03,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/markers.fasta)
[2023-06-04 19:19:03,881] [INFO] Task started: Blastn
[2023-06-04 19:19:03,881] [INFO] Running command: blastn -query GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7c0307-03c9-41e3-8849-24568b0e6b3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:19:04,856] [INFO] Task succeeded: Blastn
[2023-06-04 19:19:04,861] [INFO] Selected 25 target genomes.
[2023-06-04 19:19:04,861] [INFO] Target genome list was writen to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:19:05,024] [INFO] Task started: fastANI
[2023-06-04 19:19:05,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg93c89d53-db01-493b-92a0-84239b1d386d/GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna.gz --refList GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/target_genomes_gtdb.txt --output GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:19:14,827] [INFO] Task succeeded: fastANI
[2023-06-04 19:19:14,831] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:19:14,831] [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_902784165.1	s__UBA4285 sp902784165	100.0	481	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902784025.1	s__UBA4285 sp902784025	77.4875	97	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775895.1	s__UBA4285 sp902775895	76.8117	66	486	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:19:14,833] [INFO] GTDB search result was written to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/result_gtdb.tsv
[2023-06-04 19:19:14,833] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:19:14,836] [INFO] DFAST_QC result json was written to GCA_902784165.1_Rumen_uncultured_genome_RUG12934_genomic.fna/dqc_result.json
[2023-06-04 19:19:14,836] [INFO] DFAST_QC completed!
[2023-06-04 19:19:14,836] [INFO] Total running time: 0h0m45s