[2023-06-05 09:14:47,282] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:14:47,284] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:14:47,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference
[2023-06-05 09:14:49,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:14:49,277] [INFO] Task started: Prodigal
[2023-06-05 09:14:49,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg500ad5bc-8b93-4c35-8a02-4b7060861ace/GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna.gz | prodigal -d GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/cds.fna -a GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:14:53,266] [INFO] Task succeeded: Prodigal
[2023-06-05 09:14:53,266] [INFO] Task started: HMMsearch
[2023-06-05 09:14:53,266] [INFO] Running command: hmmsearch --tblout GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/reference_markers.hmm GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:14:53,489] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:14:53,491] [INFO] Found 6/6 markers.
[2023-06-05 09:14:53,513] [INFO] Query marker FASTA was written to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/markers.fasta
[2023-06-05 09:14:53,514] [INFO] Task started: Blastn
[2023-06-05 09:14:53,514] [INFO] Running command: blastn -query GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/reference_markers.fasta -out GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:14:54,120] [INFO] Task succeeded: Blastn
[2023-06-05 09:14:54,124] [INFO] Selected 32 target genomes.
[2023-06-05 09:14:54,125] [INFO] Target genome list was writen to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/target_genomes.txt
[2023-06-05 09:14:54,128] [INFO] Task started: fastANI
[2023-06-05 09:14:54,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg500ad5bc-8b93-4c35-8a02-4b7060861ace/GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna.gz --refList GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/target_genomes.txt --output GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:15:11,335] [INFO] Task succeeded: fastANI
[2023-06-05 09:15:11,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:15:11,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:15:11,338] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:15:11,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:15:11,339] [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 09:15:11,341] [INFO] DFAST Taxonomy check result was written to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/tc_result.tsv
[2023-06-05 09:15:11,342] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:15:11,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:15:11,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/checkm_data
[2023-06-05 09:15:11,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:15:11,367] [INFO] Task started: CheckM
[2023-06-05 09:15:11,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/checkm_input GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/checkm_result
[2023-06-05 09:15:30,133] [INFO] Task succeeded: CheckM
[2023-06-05 09:15:30,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:15:30,155] [INFO] ===== Completeness check finished =====
[2023-06-05 09:15:30,155] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:15:30,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/markers.fasta)
[2023-06-05 09:15:30,156] [INFO] Task started: Blastn
[2023-06-05 09:15:30,156] [INFO] Running command: blastn -query GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/markers.fasta -db /var/lib/cwl/stg32c7c224-ef2c-4aeb-b07c-31c1e38f3c66/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:15:31,001] [INFO] Task succeeded: Blastn
[2023-06-05 09:15:31,006] [INFO] Selected 8 target genomes.
[2023-06-05 09:15:31,006] [INFO] Target genome list was writen to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:15:31,007] [INFO] Task started: fastANI
[2023-06-05 09:15:31,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg500ad5bc-8b93-4c35-8a02-4b7060861ace/GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna.gz --refList GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/target_genomes_gtdb.txt --output GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:15:33,911] [INFO] Task succeeded: fastANI
[2023-06-05 09:15:33,922] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:15:33,923] [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_900317985.1	s__RUG420 sp900317985	98.8352	427	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	99.01	98.76	0.89	0.86	49	conclusive
GCA_017433225.1	s__RUG420 sp017433225	93.3414	436	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	96.27	96.19	0.87	0.81	5	-
GCA_017461005.1	s__RUG420 sp017461005	90.0502	411	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317085.1	s__RUG420 sp900317085	89.5475	406	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.92	97.74	0.88	0.83	42	-
GCA_904502175.1	s__RUG420 sp904502175	84.1263	284	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017614275.1	s__RUG420 sp017614275	83.4317	204	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476565.1	s__RUG420 sp017476565	82.3368	253	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.44	98.44	0.71	0.71	2	-
GCA_900542575.1	s__RUG420 sp900542575	77.2532	98	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.00	97.44	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-05 09:15:33,924] [INFO] GTDB search result was written to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/result_gtdb.tsv
[2023-06-05 09:15:33,925] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:15:33,927] [INFO] DFAST_QC result json was written to GCA_902784375.1_Rumen_uncultured_genome_RUG12966_genomic.fna/dqc_result.json
[2023-06-05 09:15:33,928] [INFO] DFAST_QC completed!
[2023-06-05 09:15:33,928] [INFO] Total running time: 0h0m47s