[2023-06-05 23:35:58,809] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:35:58,812] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:35:58,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference
[2023-06-05 23:36:00,231] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:36:00,232] [INFO] Task started: Prodigal
[2023-06-05 23:36:00,232] [INFO] Running command: gunzip -c /var/lib/cwl/stgb86bd2d9-4995-42d6-9744-6c0c30579320/GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna.gz | prodigal -d GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/cds.fna -a GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:36:05,507] [INFO] Task succeeded: Prodigal
[2023-06-05 23:36:05,507] [INFO] Task started: HMMsearch
[2023-06-05 23:36:05,507] [INFO] Running command: hmmsearch --tblout GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/reference_markers.hmm GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:36:05,919] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:36:05,920] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb86bd2d9-4995-42d6-9744-6c0c30579320/GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna.gz]
[2023-06-05 23:36:05,953] [INFO] Query marker FASTA was written to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/markers.fasta
[2023-06-05 23:36:05,953] [INFO] Task started: Blastn
[2023-06-05 23:36:05,953] [INFO] Running command: blastn -query GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/reference_markers.fasta -out GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:36:06,706] [INFO] Task succeeded: Blastn
[2023-06-05 23:36:06,718] [INFO] Selected 27 target genomes.
[2023-06-05 23:36:06,719] [INFO] Target genome list was writen to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/target_genomes.txt
[2023-06-05 23:36:06,724] [INFO] Task started: fastANI
[2023-06-05 23:36:06,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86bd2d9-4995-42d6-9744-6c0c30579320/GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna.gz --refList GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/target_genomes.txt --output GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:36:29,132] [INFO] Task succeeded: fastANI
[2023-06-05 23:36:29,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:36:29,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:36:29,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:36:29,135] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:36:29,135] [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 23:36:29,137] [INFO] DFAST Taxonomy check result was written to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/tc_result.tsv
[2023-06-05 23:36:29,138] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:36:29,138] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:36:29,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/checkm_data
[2023-06-05 23:36:29,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:36:29,178] [INFO] Task started: CheckM
[2023-06-05 23:36:29,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/checkm_input GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/checkm_result
[2023-06-05 23:36:53,225] [INFO] Task succeeded: CheckM
[2023-06-05 23:36:53,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:36:53,284] [INFO] ===== Completeness check finished =====
[2023-06-05 23:36:53,284] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:36:53,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/markers.fasta)
[2023-06-05 23:36:53,285] [INFO] Task started: Blastn
[2023-06-05 23:36:53,285] [INFO] Running command: blastn -query GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb97487b-c788-45e2-870a-74205dbc6b96/dqc_reference/reference_markers_gtdb.fasta -out GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:36:54,620] [INFO] Task succeeded: Blastn
[2023-06-05 23:36:54,624] [INFO] Selected 7 target genomes.
[2023-06-05 23:36:54,624] [INFO] Target genome list was writen to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:36:54,631] [INFO] Task started: fastANI
[2023-06-05 23:36:54,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgb86bd2d9-4995-42d6-9744-6c0c30579320/GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna.gz --refList GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/target_genomes_gtdb.txt --output GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:36:58,173] [INFO] Task succeeded: fastANI
[2023-06-05 23:36:58,189] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:36:58,189] [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_900317085.1	s__RUG420 sp900317085	98.963	474	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.92	97.74	0.88	0.83	42	conclusive
GCA_017461005.1	s__RUG420 sp017461005	91.1562	447	541	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_017433225.1	s__RUG420 sp017433225	89.4738	466	541	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_900317985.1	s__RUG420 sp900317985	89.4483	434	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	99.01	98.76	0.89	0.86	49	-
GCA_904502175.1	s__RUG420 sp904502175	83.9605	281	541	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	82.674	222	541	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	82.5573	268	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RUG420	95.0	98.44	98.44	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-06-05 23:36:58,192] [INFO] GTDB search result was written to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/result_gtdb.tsv
[2023-06-05 23:36:58,193] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:36:58,201] [INFO] DFAST_QC result json was written to GCA_902780655.1_Rumen_uncultured_genome_RUG12600_genomic.fna/dqc_result.json
[2023-06-05 23:36:58,202] [INFO] DFAST_QC completed!
[2023-06-05 23:36:58,202] [INFO] Total running time: 0h0m59s