[2023-06-04 17:44:23,361] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:44:23,364] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:44:23,365] [INFO] DQC Reference Directory: /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference
[2023-06-04 17:44:25,853] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:44:25,854] [INFO] Task started: Prodigal
[2023-06-04 17:44:25,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg75abfcf2-7c1f-47f1-96bf-92240a6fc051/GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna.gz | prodigal -d GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/cds.fna -a GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:44:43,425] [INFO] Task succeeded: Prodigal
[2023-06-04 17:44:43,425] [INFO] Task started: HMMsearch
[2023-06-04 17:44:43,425] [INFO] Running command: hmmsearch --tblout GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/reference_markers.hmm GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:44:43,654] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:44:43,656] [INFO] Found 6/6 markers.
[2023-06-04 17:44:43,682] [INFO] Query marker FASTA was written to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/markers.fasta
[2023-06-04 17:44:43,682] [INFO] Task started: Blastn
[2023-06-04 17:44:43,682] [INFO] Running command: blastn -query GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/reference_markers.fasta -out GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:44:44,289] [INFO] Task succeeded: Blastn
[2023-06-04 17:44:44,295] [INFO] Selected 26 target genomes.
[2023-06-04 17:44:44,296] [INFO] Target genome list was writen to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/target_genomes.txt
[2023-06-04 17:44:44,313] [INFO] Task started: fastANI
[2023-06-04 17:44:44,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg75abfcf2-7c1f-47f1-96bf-92240a6fc051/GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna.gz --refList GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/target_genomes.txt --output GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:44:57,613] [INFO] Task succeeded: fastANI
[2023-06-04 17:44:57,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:44:57,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:44:57,621] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:44:57,622] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:44:57,622] [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
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.4149	53	815	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:44:57,624] [INFO] DFAST Taxonomy check result was written to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/tc_result.tsv
[2023-06-04 17:44:57,625] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:44:57,625] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:44:57,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/checkm_data
[2023-06-04 17:44:57,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:44:57,658] [INFO] Task started: CheckM
[2023-06-04 17:44:57,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/checkm_input GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/checkm_result
[2023-06-04 17:45:51,987] [INFO] Task succeeded: CheckM
[2023-06-04 17:45:51,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:45:52,014] [INFO] ===== Completeness check finished =====
[2023-06-04 17:45:52,014] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:45:52,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/markers.fasta)
[2023-06-04 17:45:52,015] [INFO] Task started: Blastn
[2023-06-04 17:45:52,015] [INFO] Running command: blastn -query GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/markers.fasta -db /var/lib/cwl/stgef4ff764-a12e-40e2-a546-ef383eb5df8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:45:52,868] [INFO] Task succeeded: Blastn
[2023-06-04 17:45:52,874] [INFO] Selected 11 target genomes.
[2023-06-04 17:45:52,874] [INFO] Target genome list was writen to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:45:52,951] [INFO] Task started: fastANI
[2023-06-04 17:45:52,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg75abfcf2-7c1f-47f1-96bf-92240a6fc051/GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna.gz --refList GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/target_genomes_gtdb.txt --output GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:45:59,681] [INFO] Task succeeded: fastANI
[2023-06-04 17:45:59,701] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:45:59,702] [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_900316505.1	s__UBA4334 sp900316505	97.9702	745	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.14	0.89	0.83	54	conclusive
GCA_900316975.1	s__UBA4334 sp900316975	83.9025	553	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.29	0.86	0.80	13	-
GCA_902768125.1	s__UBA4334 sp902768125	82.5334	537	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_905235525.1	s__UBA4334 sp905235525	82.5156	492	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.02	99.02	0.89	0.89	2	-
GCA_902801475.1	s__UBA4334 sp902801475	82.3773	498	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.71	97.36	0.83	0.79	15	-
GCA_017651245.1	s__UBA4334 sp017651245	81.981	500	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017614895.1	s__UBA4334 sp017614895	81.8782	466	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017448965.1	s__UBA4334 sp017448965	80.7936	377	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617805.1	s__UBA4334 sp017617805	80.2596	296	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470525.1	s__UBA4334 sp017470525	80.0588	349	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483605.1	s__UBA4334 sp017483605	79.9594	310	815	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-04 17:45:59,704] [INFO] GTDB search result was written to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/result_gtdb.tsv
[2023-06-04 17:45:59,705] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:45:59,710] [INFO] DFAST_QC result json was written to GCA_902769745.1_Rumen_uncultured_genome_RUG11494_genomic.fna/dqc_result.json
[2023-06-04 17:45:59,711] [INFO] DFAST_QC completed!
[2023-06-04 17:45:59,711] [INFO] Total running time: 0h1m36s