[2023-06-05 08:49:01,074] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:49:01,077] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:49:01,077] [INFO] DQC Reference Directory: /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference
[2023-06-05 08:49:02,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:49:02,394] [INFO] Task started: Prodigal
[2023-06-05 08:49:02,394] [INFO] Running command: gunzip -c /var/lib/cwl/stgbac9bad7-23d2-47f8-a917-8cafe565fa92/GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna.gz | prodigal -d GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/cds.fna -a GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:49:16,410] [INFO] Task succeeded: Prodigal
[2023-06-05 08:49:16,411] [INFO] Task started: HMMsearch
[2023-06-05 08:49:16,411] [INFO] Running command: hmmsearch --tblout GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/reference_markers.hmm GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:49:16,677] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:49:16,678] [INFO] Found 6/6 markers.
[2023-06-05 08:49:16,713] [INFO] Query marker FASTA was written to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/markers.fasta
[2023-06-05 08:49:16,714] [INFO] Task started: Blastn
[2023-06-05 08:49:16,714] [INFO] Running command: blastn -query GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/markers.fasta -db /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/reference_markers.fasta -out GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:17,391] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:17,395] [INFO] Selected 26 target genomes.
[2023-06-05 08:49:17,396] [INFO] Target genome list was writen to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/target_genomes.txt
[2023-06-05 08:49:17,397] [INFO] Task started: fastANI
[2023-06-05 08:49:17,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac9bad7-23d2-47f8-a917-8cafe565fa92/GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna.gz --refList GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/target_genomes.txt --output GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:49:32,817] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:32,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:49:32,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:49:32,820] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:49:32,820] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:49:32,821] [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 08:49:32,823] [INFO] DFAST Taxonomy check result was written to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/tc_result.tsv
[2023-06-05 08:49:32,823] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:49:32,823] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:49:32,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/checkm_data
[2023-06-05 08:49:32,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:49:32,856] [INFO] Task started: CheckM
[2023-06-05 08:49:32,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/checkm_input GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/checkm_result
[2023-06-05 08:50:14,294] [INFO] Task succeeded: CheckM
[2023-06-05 08:50:14,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:50:14,316] [INFO] ===== Completeness check finished =====
[2023-06-05 08:50:14,316] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:50:14,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/markers.fasta)
[2023-06-05 08:50:14,317] [INFO] Task started: Blastn
[2023-06-05 08:50:14,317] [INFO] Running command: blastn -query GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/markers.fasta -db /var/lib/cwl/stged11a79a-792a-4936-aeec-1f3111a58f3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:50:15,182] [INFO] Task succeeded: Blastn
[2023-06-05 08:50:15,187] [INFO] Selected 20 target genomes.
[2023-06-05 08:50:15,188] [INFO] Target genome list was writen to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:50:15,190] [INFO] Task started: fastANI
[2023-06-05 08:50:15,190] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac9bad7-23d2-47f8-a917-8cafe565fa92/GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna.gz --refList GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/target_genomes_gtdb.txt --output GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:50:22,930] [INFO] Task succeeded: fastANI
[2023-06-05 08:50:22,946] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:50:22,947] [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_900317925.1	s__Cryptobacteroides sp900317925	96.3394	579	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	96.11	0.85	0.74	52	conclusive
GCA_902799895.1	s__Cryptobacteroides sp902799895	92.2101	510	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.23	98.23	0.80	0.80	2	-
GCA_900317845.1	s__Cryptobacteroides sp900317845	78.3903	146	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.57	95.18	0.88	0.74	22	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	77.959	159	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	77.6599	170	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	77.6048	143	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_900319405.1	s__Cryptobacteroides sp900319405	77.5853	136	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	77.5481	146	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_017471025.1	s__Cryptobacteroides sp017471025	77.5478	126	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290835.1	s__Cryptobacteroides sp016290835	77.4526	127	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	77.368	119	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_017427385.1	s__Cryptobacteroides sp017427385	77.2959	100	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	77.2868	94	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	77.1346	140	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780935.1	s__Cryptobacteroides sp902780935	77.0277	92	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.9118	129	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.42	97.90	0.88	0.86	3	-
GCA_900320185.1	s__Cryptobacteroides sp900320185	76.874	98	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_902766985.1	s__Cryptobacteroides sp902766985	76.736	75	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.09	97.97	0.82	0.68	3	-
GCA_902796455.1	s__Cryptobacteroides sp902796455	76.4898	96	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453565.1	s__Cryptobacteroides sp017453565	76.4429	122	762	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:50:22,949] [INFO] GTDB search result was written to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/result_gtdb.tsv
[2023-06-05 08:50:22,949] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:50:22,954] [INFO] DFAST_QC result json was written to GCA_902784255.1_Rumen_uncultured_genome_RUG12963_genomic.fna/dqc_result.json
[2023-06-05 08:50:22,954] [INFO] DFAST_QC completed!
[2023-06-05 08:50:22,955] [INFO] Total running time: 0h1m22s