[2023-06-04 20:01:52,110] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:01:52,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:01:52,117] [INFO] DQC Reference Directory: /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference
[2023-06-04 20:01:53,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:01:53,439] [INFO] Task started: Prodigal
[2023-06-04 20:01:53,439] [INFO] Running command: gunzip -c /var/lib/cwl/stge52f3eeb-1cdc-4e84-9438-484a291ed689/GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna.gz | prodigal -d GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/cds.fna -a GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:02:00,506] [INFO] Task succeeded: Prodigal
[2023-06-04 20:02:00,507] [INFO] Task started: HMMsearch
[2023-06-04 20:02:00,507] [INFO] Running command: hmmsearch --tblout GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/reference_markers.hmm GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:02:00,698] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:02:00,699] [INFO] Found 6/6 markers.
[2023-06-04 20:02:00,727] [INFO] Query marker FASTA was written to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/markers.fasta
[2023-06-04 20:02:00,728] [INFO] Task started: Blastn
[2023-06-04 20:02:00,728] [INFO] Running command: blastn -query GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/reference_markers.fasta -out GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:01,364] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:01,369] [INFO] Selected 32 target genomes.
[2023-06-04 20:02:01,369] [INFO] Target genome list was writen to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/target_genomes.txt
[2023-06-04 20:02:01,438] [INFO] Task started: fastANI
[2023-06-04 20:02:01,438] [INFO] Running command: fastANI --query /var/lib/cwl/stge52f3eeb-1cdc-4e84-9438-484a291ed689/GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna.gz --refList GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/target_genomes.txt --output GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:02:18,211] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:18,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:02:18,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:02:18,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:02:18,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:02:18,214] [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 20:02:18,216] [INFO] DFAST Taxonomy check result was written to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/tc_result.tsv
[2023-06-04 20:02:18,216] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:02:18,217] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:02:18,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/checkm_data
[2023-06-04 20:02:18,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:02:18,249] [INFO] Task started: CheckM
[2023-06-04 20:02:18,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/checkm_input GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/checkm_result
[2023-06-04 20:02:43,745] [INFO] Task succeeded: CheckM
[2023-06-04 20:02:43,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:02:43,764] [INFO] ===== Completeness check finished =====
[2023-06-04 20:02:43,764] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:02:43,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/markers.fasta)
[2023-06-04 20:02:43,765] [INFO] Task started: Blastn
[2023-06-04 20:02:43,765] [INFO] Running command: blastn -query GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/markers.fasta -db /var/lib/cwl/stgaef1d194-6509-45e2-8ccd-4e15e6903e76/dqc_reference/reference_markers_gtdb.fasta -out GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:44,800] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:44,804] [INFO] Selected 10 target genomes.
[2023-06-04 20:02:44,804] [INFO] Target genome list was writen to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:02:44,809] [INFO] Task started: fastANI
[2023-06-04 20:02:44,809] [INFO] Running command: fastANI --query /var/lib/cwl/stge52f3eeb-1cdc-4e84-9438-484a291ed689/GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna.gz --refList GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/target_genomes_gtdb.txt --output GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:02:49,710] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:49,719] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:02:49,719] [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_902786285.1	s__UBA6857 sp902786285	96.9339	640	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	96.81	96.53	0.83	0.83	3	conclusive
GCA_902761265.1	s__UBA6857 sp902761265	90.9853	532	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290665.1	s__UBA6857 sp016290665	82.5683	476	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017544665.1	s__UBA6857 sp017544665	81.526	453	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792985.1	s__UBA6857 sp902792985	80.3303	351	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774035.1	s__UBA6857 sp902774035	79.8794	321	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434855.1	s__UBA6857 sp017434855	79.3961	348	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	98.64	98.64	0.90	0.90	2	-
GCA_902772935.1	s__UBA6857 sp902772935	78.69	264	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA6857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796315.1	s__DTU089 sp902796315	76.2896	68	780	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__DTU089	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:02:49,722] [INFO] GTDB search result was written to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/result_gtdb.tsv
[2023-06-04 20:02:49,722] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:02:49,726] [INFO] DFAST_QC result json was written to GCA_902790155.1_Rumen_uncultured_genome_RUG13540_genomic.fna/dqc_result.json
[2023-06-04 20:02:49,726] [INFO] DFAST_QC completed!
[2023-06-04 20:02:49,726] [INFO] Total running time: 0h0m58s