[2023-06-05 09:25:48,473] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:48,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:48,476] [INFO] DQC Reference Directory: /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference
[2023-06-05 09:25:50,431] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:50,432] [INFO] Task started: Prodigal
[2023-06-05 09:25:50,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgef5ddd51-8697-4ea6-810e-41b23a0973ab/GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna.gz | prodigal -d GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/cds.fna -a GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:54,525] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:54,525] [INFO] Task started: HMMsearch
[2023-06-05 09:25:54,525] [INFO] Running command: hmmsearch --tblout GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/reference_markers.hmm GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:54,762] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:54,764] [INFO] Found 6/6 markers.
[2023-06-05 09:25:54,797] [INFO] Query marker FASTA was written to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/markers.fasta
[2023-06-05 09:25:54,798] [INFO] Task started: Blastn
[2023-06-05 09:25:54,798] [INFO] Running command: blastn -query GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/markers.fasta -db /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/reference_markers.fasta -out GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:55,429] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:55,433] [INFO] Selected 21 target genomes.
[2023-06-05 09:25:55,434] [INFO] Target genome list was writen to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/target_genomes.txt
[2023-06-05 09:25:55,440] [INFO] Task started: fastANI
[2023-06-05 09:25:55,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ddd51-8697-4ea6-810e-41b23a0973ab/GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna.gz --refList GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/target_genomes.txt --output GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:26:08,016] [INFO] Task succeeded: fastANI
[2023-06-05 09:26:08,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:26:08,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:26:08,019] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:26:08,019] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:26:08,019] [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 09:26:08,022] [INFO] DFAST Taxonomy check result was written to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/tc_result.tsv
[2023-06-05 09:26:08,022] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:26:08,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:26:08,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/checkm_data
[2023-06-05 09:26:08,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:26:08,054] [INFO] Task started: CheckM
[2023-06-05 09:26:08,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/checkm_input GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/checkm_result
[2023-06-05 09:26:27,649] [INFO] Task succeeded: CheckM
[2023-06-05 09:26:27,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.14%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:26:27,672] [INFO] ===== Completeness check finished =====
[2023-06-05 09:26:27,672] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:26:27,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/markers.fasta)
[2023-06-05 09:26:27,673] [INFO] Task started: Blastn
[2023-06-05 09:26:27,673] [INFO] Running command: blastn -query GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/markers.fasta -db /var/lib/cwl/stgf409579e-7f14-4fb0-ae9a-d37a930cd9fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:26:28,722] [INFO] Task succeeded: Blastn
[2023-06-05 09:26:28,726] [INFO] Selected 11 target genomes.
[2023-06-05 09:26:28,726] [INFO] Target genome list was writen to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:26:28,733] [INFO] Task started: fastANI
[2023-06-05 09:26:28,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5ddd51-8697-4ea6-810e-41b23a0973ab/GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna.gz --refList GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/target_genomes_gtdb.txt --output GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:26:33,733] [INFO] Task succeeded: fastANI
[2023-06-05 09:26:33,741] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:26:33,742] [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_902797235.1	s__UBA1248 sp902797235	98.4638	490	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	98.46	98.46	0.90	0.90	2	conclusive
GCA_902782785.1	s__UBA1248 sp902782785	81.4699	339	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	97.78	97.78	0.92	0.92	2	-
GCA_902784545.1	s__UBA1248 sp902784545	80.4399	321	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280525.1	s__UBA1248 sp016280525	79.8863	240	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017443595.1	s__UBA1248 sp017443595	79.7966	294	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002308615.1	s__UBA1248 sp002308615	79.669	289	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619885.1	s__UBA1248 sp017619885	78.7887	255	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958705.1	s__UBA1248 sp017958705	78.703	230	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778145.1	s__UBA1248 sp902778145	78.364	211	547	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UBA1248	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:26:33,743] [INFO] GTDB search result was written to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/result_gtdb.tsv
[2023-06-05 09:26:33,746] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:26:33,749] [INFO] DFAST_QC result json was written to GCA_902783045.1_Rumen_uncultured_genome_RUG12828_genomic.fna/dqc_result.json
[2023-06-05 09:26:33,750] [INFO] DFAST_QC completed!
[2023-06-05 09:26:33,750] [INFO] Total running time: 0h0m45s