[2023-06-07 18:14:52,481] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:14:52,490] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:14:52,491] [INFO] DQC Reference Directory: /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference
[2023-06-07 18:14:54,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:14:54,119] [INFO] Task started: Prodigal
[2023-06-07 18:14:54,119] [INFO] Running command: gunzip -c /var/lib/cwl/stgff716d91-1946-4441-9662-b57f8ddb7f8b/GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna.gz | prodigal -d GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/cds.fna -a GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:15:05,306] [INFO] Task succeeded: Prodigal
[2023-06-07 18:15:05,307] [INFO] Task started: HMMsearch
[2023-06-07 18:15:05,307] [INFO] Running command: hmmsearch --tblout GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/reference_markers.hmm GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:15:05,569] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:15:05,570] [INFO] Found 6/6 markers.
[2023-06-07 18:15:05,599] [INFO] Query marker FASTA was written to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/markers.fasta
[2023-06-07 18:15:05,600] [INFO] Task started: Blastn
[2023-06-07 18:15:05,600] [INFO] Running command: blastn -query GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/markers.fasta -db /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/reference_markers.fasta -out GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:06,184] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:06,189] [INFO] Selected 30 target genomes.
[2023-06-07 18:15:06,190] [INFO] Target genome list was writen to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/target_genomes.txt
[2023-06-07 18:15:06,196] [INFO] Task started: fastANI
[2023-06-07 18:15:06,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgff716d91-1946-4441-9662-b57f8ddb7f8b/GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna.gz --refList GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/target_genomes.txt --output GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:15:25,720] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:25,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:15:25,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:15:25,723] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:15:25,723] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:15:25,724] [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
--------------------------------------------------------------------------------
[2023-06-07 18:15:25,726] [INFO] DFAST Taxonomy check result was written to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/tc_result.tsv
[2023-06-07 18:15:25,726] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:15:25,727] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:15:25,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/checkm_data
[2023-06-07 18:15:25,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:15:25,756] [INFO] Task started: CheckM
[2023-06-07 18:15:25,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/checkm_input GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/checkm_result
[2023-06-07 18:16:00,867] [INFO] Task succeeded: CheckM
[2023-06-07 18:16:00,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:16:00,886] [INFO] ===== Completeness check finished =====
[2023-06-07 18:16:00,887] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:16:00,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/markers.fasta)
[2023-06-07 18:16:00,887] [INFO] Task started: Blastn
[2023-06-07 18:16:00,888] [INFO] Running command: blastn -query GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/markers.fasta -db /var/lib/cwl/stga253e040-4bcf-4b25-8885-7a30015c245e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:16:01,761] [INFO] Task succeeded: Blastn
[2023-06-07 18:16:01,766] [INFO] Selected 23 target genomes.
[2023-06-07 18:16:01,766] [INFO] Target genome list was writen to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:16:01,779] [INFO] Task started: fastANI
[2023-06-07 18:16:01,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgff716d91-1946-4441-9662-b57f8ddb7f8b/GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna.gz --refList GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/target_genomes_gtdb.txt --output GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:16:10,065] [INFO] Task succeeded: fastANI
[2023-06-07 18:16:10,086] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:16:10,086] [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	97.9946	464	521	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	91.9619	395	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.23	98.23	0.80	0.80	2	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	77.9207	124	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471025.1	s__Cryptobacteroides sp017471025	77.777	100	521	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	77.7074	98	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	77.5897	65	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	77.4782	87	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	77.4118	138	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	77.305	98	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	77.2447	115	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	77.2418	101	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	77.1665	98	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283985.1	s__Cryptobacteroides sp016283985	77.0363	69	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	77.0202	99	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_017453565.1	s__Cryptobacteroides sp017453565	77.0156	89	521	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	76.962	63	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	97.52	0.84	0.84	2	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	76.9081	74	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_902796455.1	s__Cryptobacteroides sp902796455	76.8324	77	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.7584	106	521	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	76.5131	70	521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
--------------------------------------------------------------------------------
[2023-06-07 18:16:10,088] [INFO] GTDB search result was written to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/result_gtdb.tsv
[2023-06-07 18:16:10,089] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:16:10,093] [INFO] DFAST_QC result json was written to GCA_902757445.1_Rumen_uncultured_genome_RUG10266_genomic.fna/dqc_result.json
[2023-06-07 18:16:10,093] [INFO] DFAST_QC completed!
[2023-06-07 18:16:10,093] [INFO] Total running time: 0h1m18s