[2023-06-05 18:47:29,833] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:47:29,835] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:47:29,835] [INFO] DQC Reference Directory: /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference
[2023-06-05 18:47:31,569] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:47:31,570] [INFO] Task started: Prodigal
[2023-06-05 18:47:31,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg9916230d-507f-4980-9d70-f3d57bb425c2/GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna.gz | prodigal -d GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/cds.fna -a GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:47:33,790] [INFO] Task succeeded: Prodigal
[2023-06-05 18:47:33,790] [INFO] Task started: HMMsearch
[2023-06-05 18:47:33,790] [INFO] Running command: hmmsearch --tblout GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/reference_markers.hmm GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:47:34,116] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:47:34,117] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9916230d-507f-4980-9d70-f3d57bb425c2/GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna.gz]
[2023-06-05 18:47:34,134] [INFO] Query marker FASTA was written to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/markers.fasta
[2023-06-05 18:47:34,134] [INFO] Task started: Blastn
[2023-06-05 18:47:34,135] [INFO] Running command: blastn -query GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/reference_markers.fasta -out GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:47:34,780] [INFO] Task succeeded: Blastn
[2023-06-05 18:47:34,784] [INFO] Selected 23 target genomes.
[2023-06-05 18:47:34,784] [INFO] Target genome list was writen to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/target_genomes.txt
[2023-06-05 18:47:34,793] [INFO] Task started: fastANI
[2023-06-05 18:47:34,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg9916230d-507f-4980-9d70-f3d57bb425c2/GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna.gz --refList GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/target_genomes.txt --output GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:47:45,753] [INFO] Task succeeded: fastANI
[2023-06-05 18:47:45,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:47:45,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:47:45,756] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:47:45,756] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:47:45,756] [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 18:47:45,758] [INFO] DFAST Taxonomy check result was written to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/tc_result.tsv
[2023-06-05 18:47:45,758] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:47:45,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:47:45,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/checkm_data
[2023-06-05 18:47:45,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:47:45,776] [INFO] Task started: CheckM
[2023-06-05 18:47:45,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/checkm_input GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/checkm_result
[2023-06-05 18:48:08,081] [INFO] Task succeeded: CheckM
[2023-06-05 18:48:08,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:48:08,100] [INFO] ===== Completeness check finished =====
[2023-06-05 18:48:08,100] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:48:08,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/markers.fasta)
[2023-06-05 18:48:08,101] [INFO] Task started: Blastn
[2023-06-05 18:48:08,101] [INFO] Running command: blastn -query GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/markers.fasta -db /var/lib/cwl/stgea9eaffc-6d99-4604-92a9-53ec40a38a0f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:48:08,877] [INFO] Task succeeded: Blastn
[2023-06-05 18:48:08,881] [INFO] Selected 15 target genomes.
[2023-06-05 18:48:08,881] [INFO] Target genome list was writen to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:48:08,896] [INFO] Task started: fastANI
[2023-06-05 18:48:08,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg9916230d-507f-4980-9d70-f3d57bb425c2/GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna.gz --refList GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/target_genomes_gtdb.txt --output GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:48:13,825] [INFO] Task succeeded: fastANI
[2023-06-05 18:48:13,832] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:48:13,833] [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_902797855.1	s__UBA3207 sp902797855	100.0	347	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902787955.1	s__UBA3207 sp902787955	78.3796	124	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	95.98	95.98	0.91	0.91	2	-
GCA_902768335.1	s__UBA3207 sp902768335	78.005	77	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	95.94	95.94	0.84	0.84	2	-
GCA_902774655.1	s__UBA3207 sp902774655	77.9601	51	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314585.1	s__UBA3207 sp900314585	77.6669	85	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	98.34	96.67	0.96	0.93	3	-
GCA_902796125.1	s__UBA3207 sp902796125	77.5526	81	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003501485.1	s__UBA3207 sp003501485	77.1614	54	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:48:13,835] [INFO] GTDB search result was written to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/result_gtdb.tsv
[2023-06-05 18:48:13,836] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:48:13,839] [INFO] DFAST_QC result json was written to GCA_902797855.1_Rumen_uncultured_genome_RUG14309_genomic.fna/dqc_result.json
[2023-06-05 18:48:13,839] [INFO] DFAST_QC completed!
[2023-06-05 18:48:13,839] [INFO] Total running time: 0h0m44s