[2023-06-05 09:56:34,252] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:56:34,256] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:56:34,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference
[2023-06-05 09:56:35,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:56:35,555] [INFO] Task started: Prodigal
[2023-06-05 09:56:35,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg075fc89f-9bb7-42d9-85de-2b9e973d2d6c/GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna.gz | prodigal -d GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/cds.fna -a GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:56:39,652] [INFO] Task succeeded: Prodigal
[2023-06-05 09:56:39,653] [INFO] Task started: HMMsearch
[2023-06-05 09:56:39,653] [INFO] Running command: hmmsearch --tblout GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/reference_markers.hmm GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:56:39,887] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:56:39,895] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg075fc89f-9bb7-42d9-85de-2b9e973d2d6c/GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna.gz]
[2023-06-05 09:56:39,914] [INFO] Query marker FASTA was written to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/markers.fasta
[2023-06-05 09:56:39,914] [INFO] Task started: Blastn
[2023-06-05 09:56:39,914] [INFO] Running command: blastn -query GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/reference_markers.fasta -out GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:56:40,601] [INFO] Task succeeded: Blastn
[2023-06-05 09:56:40,628] [INFO] Selected 25 target genomes.
[2023-06-05 09:56:40,629] [INFO] Target genome list was writen to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/target_genomes.txt
[2023-06-05 09:56:40,635] [INFO] Task started: fastANI
[2023-06-05 09:56:40,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg075fc89f-9bb7-42d9-85de-2b9e973d2d6c/GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna.gz --refList GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/target_genomes.txt --output GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:56:59,336] [INFO] Task succeeded: fastANI
[2023-06-05 09:56:59,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:56:59,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:56:59,340] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:56:59,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:56:59,340] [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 09:56:59,343] [INFO] DFAST Taxonomy check result was written to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/tc_result.tsv
[2023-06-05 09:56:59,343] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:56:59,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:56:59,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/checkm_data
[2023-06-05 09:56:59,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:56:59,372] [INFO] Task started: CheckM
[2023-06-05 09:56:59,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/checkm_input GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/checkm_result
[2023-06-05 09:57:19,426] [INFO] Task succeeded: CheckM
[2023-06-05 09:57:19,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:57:19,450] [INFO] ===== Completeness check finished =====
[2023-06-05 09:57:19,451] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:57:19,451] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/markers.fasta)
[2023-06-05 09:57:19,451] [INFO] Task started: Blastn
[2023-06-05 09:57:19,452] [INFO] Running command: blastn -query GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2de211-1976-42b6-b018-e51f140495f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:57:20,250] [INFO] Task succeeded: Blastn
[2023-06-05 09:57:20,255] [INFO] Selected 21 target genomes.
[2023-06-05 09:57:20,256] [INFO] Target genome list was writen to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:57:20,266] [INFO] Task started: fastANI
[2023-06-05 09:57:20,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg075fc89f-9bb7-42d9-85de-2b9e973d2d6c/GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna.gz --refList GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/target_genomes_gtdb.txt --output GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:57:26,677] [INFO] Task succeeded: fastANI
[2023-06-05 09:57:26,684] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:57:26,684] [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_902790905.1	s__RUG13615 sp902790905	97.6815	369	418	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG13615	95.0	97.66	97.36	0.88	0.87	5	conclusive
GCA_902803185.1	s__Eubacterium_B sp902803185	76.2827	52	418	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Eubacterium_B	95.0	98.04	98.04	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2023-06-05 09:57:26,687] [INFO] GTDB search result was written to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/result_gtdb.tsv
[2023-06-05 09:57:26,687] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:57:26,690] [INFO] DFAST_QC result json was written to GCA_902792265.1_Rumen_uncultured_genome_RUG13753_genomic.fna/dqc_result.json
[2023-06-05 09:57:26,690] [INFO] DFAST_QC completed!
[2023-06-05 09:57:26,690] [INFO] Total running time: 0h0m52s