[2023-06-08 19:34:42,205] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:34:42,227] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:34:42,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference
[2023-06-08 19:34:44,152] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:34:44,153] [INFO] Task started: Prodigal
[2023-06-08 19:34:44,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cce62e6-c2a8-41ee-8e71-e5e772608555/GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna.gz | prodigal -d GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/cds.fna -a GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:34:48,176] [INFO] Task succeeded: Prodigal
[2023-06-08 19:34:48,176] [INFO] Task started: HMMsearch
[2023-06-08 19:34:48,176] [INFO] Running command: hmmsearch --tblout GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/reference_markers.hmm GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:34:48,420] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:34:48,422] [INFO] Found 6/6 markers.
[2023-06-08 19:34:48,442] [INFO] Query marker FASTA was written to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/markers.fasta
[2023-06-08 19:34:48,442] [INFO] Task started: Blastn
[2023-06-08 19:34:48,442] [INFO] Running command: blastn -query GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/reference_markers.fasta -out GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:49,089] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:49,093] [INFO] Selected 25 target genomes.
[2023-06-08 19:34:49,093] [INFO] Target genome list was writen to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/target_genomes.txt
[2023-06-08 19:34:49,099] [INFO] Task started: fastANI
[2023-06-08 19:34:49,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cce62e6-c2a8-41ee-8e71-e5e772608555/GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna.gz --refList GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/target_genomes.txt --output GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:34:59,410] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:59,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:34:59,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:34:59,414] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:34:59,414] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:34:59,414] [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
--------------------------------------------------------------------------------
[2023-06-08 19:34:59,421] [INFO] DFAST Taxonomy check result was written to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/tc_result.tsv
[2023-06-08 19:34:59,422] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:34:59,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:34:59,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/checkm_data
[2023-06-08 19:34:59,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:34:59,449] [INFO] Task started: CheckM
[2023-06-08 19:34:59,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/checkm_input GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/checkm_result
[2023-06-08 19:35:18,605] [INFO] Task succeeded: CheckM
[2023-06-08 19:35:18,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:35:18,627] [INFO] ===== Completeness check finished =====
[2023-06-08 19:35:18,627] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:35:18,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/markers.fasta)
[2023-06-08 19:35:18,628] [INFO] Task started: Blastn
[2023-06-08 19:35:18,628] [INFO] Running command: blastn -query GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52a1cfc-bb96-4ba9-9dca-6818c0f200d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:35:19,676] [INFO] Task succeeded: Blastn
[2023-06-08 19:35:19,680] [INFO] Selected 16 target genomes.
[2023-06-08 19:35:19,681] [INFO] Target genome list was writen to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:35:19,688] [INFO] Task started: fastANI
[2023-06-08 19:35:19,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cce62e6-c2a8-41ee-8e71-e5e772608555/GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna.gz --refList GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/target_genomes_gtdb.txt --output GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:35:23,983] [INFO] Task succeeded: fastANI
[2023-06-08 19:35:23,992] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:35:23,992] [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_902763535.1	s__CAZU01 sp902763535	100.0	500	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	97.09	97.09	0.93	0.93	2	conclusive
GCA_902799835.1	s__CAZU01 sp902799835	89.0131	442	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761535.1	s__CAZU01 sp902761535	80.0993	263	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.62	98.62	0.96	0.96	2	-
GCA_017470165.1	s__CAZU01 sp017470165	77.7626	149	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761715.1	s__51-20 sp902761715	77.6331	63	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501665.1	s__CAZU01 sp017501665	77.4667	122	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778645.1	s__Scatocola sp902778645	77.205	53	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__Scatocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062585.1	s__CAZU01 sp015062585	77.1989	128	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.10	98.10	0.95	0.95	3	-
GCA_000432275.1	s__CAZU01 sp000432275	76.162	56	500	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAZU01	95.0	98.86	98.76	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2023-06-08 19:35:23,995] [INFO] GTDB search result was written to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/result_gtdb.tsv
[2023-06-08 19:35:23,995] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:35:23,998] [INFO] DFAST_QC result json was written to GCA_902763535.1_Rumen_uncultured_genome_RUG10873_genomic.fna/dqc_result.json
[2023-06-08 19:35:23,999] [INFO] DFAST_QC completed!
[2023-06-08 19:35:23,999] [INFO] Total running time: 0h0m42s