[2023-06-07 20:40:13,626] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:13,633] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:13,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference
[2023-06-07 20:40:14,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:14,919] [INFO] Task started: Prodigal
[2023-06-07 20:40:14,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg217f59cb-894a-4f99-8489-7c3f56f4e4f0/GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna.gz | prodigal -d GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/cds.fna -a GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:20,277] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:20,278] [INFO] Task started: HMMsearch
[2023-06-07 20:40:20,278] [INFO] Running command: hmmsearch --tblout GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/reference_markers.hmm GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:20,516] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:20,517] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg217f59cb-894a-4f99-8489-7c3f56f4e4f0/GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna.gz]
[2023-06-07 20:40:20,545] [INFO] Query marker FASTA was written to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/markers.fasta
[2023-06-07 20:40:20,546] [INFO] Task started: Blastn
[2023-06-07 20:40:20,546] [INFO] Running command: blastn -query GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/markers.fasta -db /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/reference_markers.fasta -out GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:21,161] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:21,166] [INFO] Selected 25 target genomes.
[2023-06-07 20:40:21,166] [INFO] Target genome list was writen to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/target_genomes.txt
[2023-06-07 20:40:21,172] [INFO] Task started: fastANI
[2023-06-07 20:40:21,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg217f59cb-894a-4f99-8489-7c3f56f4e4f0/GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna.gz --refList GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/target_genomes.txt --output GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:37,078] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:37,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:37,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:37,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:37,082] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:40:37,082] [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 20:40:37,085] [INFO] DFAST Taxonomy check result was written to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/tc_result.tsv
[2023-06-07 20:40:37,086] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:37,087] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:37,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/checkm_data
[2023-06-07 20:40:37,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:37,131] [INFO] Task started: CheckM
[2023-06-07 20:40:37,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/checkm_input GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/checkm_result
[2023-06-07 20:41:01,145] [INFO] Task succeeded: CheckM
[2023-06-07 20:41:01,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:41:01,166] [INFO] ===== Completeness check finished =====
[2023-06-07 20:41:01,166] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:41:01,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/markers.fasta)
[2023-06-07 20:41:01,167] [INFO] Task started: Blastn
[2023-06-07 20:41:01,167] [INFO] Running command: blastn -query GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/markers.fasta -db /var/lib/cwl/stg67ad3f3e-77bb-4d0c-86f0-7f18dfc8ac85/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:41:02,018] [INFO] Task succeeded: Blastn
[2023-06-07 20:41:02,022] [INFO] Selected 13 target genomes.
[2023-06-07 20:41:02,023] [INFO] Target genome list was writen to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:41:02,027] [INFO] Task started: fastANI
[2023-06-07 20:41:02,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg217f59cb-894a-4f99-8489-7c3f56f4e4f0/GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna.gz --refList GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/target_genomes_gtdb.txt --output GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:41:08,581] [INFO] Task succeeded: fastANI
[2023-06-07 20:41:08,592] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:41:08,592] [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_902766435.1	s__Bulleidia sp902766435	100.0	696	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902786245.1	s__Bulleidia sp902786245	77.8011	153	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793635.1	s__Bulleidia sp902793635	77.7425	153	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000701725.1	s__Bulleidia sp000701725	77.718	151	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.69	96.78	0.88	0.87	6	-
GCA_017510405.1	s__Bulleidia sp017510405	77.6494	136	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778375.1	s__Bulleidia sp902778375	77.6178	133	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.02	97.02	0.90	0.90	2	-
GCA_017421125.1	s__Bulleidia sp017421125	77.456	80	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404505.1	s__Bulleidia sp017404505	77.4018	147	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.58	97.58	0.95	0.95	2	-
GCA_900320455.1	s__Bulleidia sp900320455	77.1104	139	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.55	97.17	0.84	0.70	5	-
GCA_902766005.1	s__Bulleidia sp902766005	77.0904	125	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539825.1	s__Bulleidia sp017539825	76.9676	105	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432325.1	s__Bulleidia sp017432325	76.9654	119	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512555.1	s__Bulleidia sp017512555	76.7073	54	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:41:08,594] [INFO] GTDB search result was written to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/result_gtdb.tsv
[2023-06-07 20:41:08,595] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:41:08,597] [INFO] DFAST_QC result json was written to GCA_902766435.1_Rumen_uncultured_genome_RUG11161_genomic.fna/dqc_result.json
[2023-06-07 20:41:08,597] [INFO] DFAST_QC completed!
[2023-06-07 20:41:08,598] [INFO] Total running time: 0h0m55s