[2023-06-08 20:04:46,360] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:46,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:46,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference
[2023-06-08 20:04:47,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:47,538] [INFO] Task started: Prodigal
[2023-06-08 20:04:47,538] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1b1b8b9-9a35-493a-881f-ec4fc66f77b6/GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna.gz | prodigal -d GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/cds.fna -a GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:53,001] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:53,001] [INFO] Task started: HMMsearch
[2023-06-08 20:04:53,002] [INFO] Running command: hmmsearch --tblout GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/reference_markers.hmm GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:53,256] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:53,257] [INFO] Found 6/6 markers.
[2023-06-08 20:04:53,285] [INFO] Query marker FASTA was written to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/markers.fasta
[2023-06-08 20:04:53,286] [INFO] Task started: Blastn
[2023-06-08 20:04:53,286] [INFO] Running command: blastn -query GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/reference_markers.fasta -out GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:54,213] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:54,218] [INFO] Selected 17 target genomes.
[2023-06-08 20:04:54,218] [INFO] Target genome list was writen to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/target_genomes.txt
[2023-06-08 20:04:54,222] [INFO] Task started: fastANI
[2023-06-08 20:04:54,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1b1b8b9-9a35-493a-881f-ec4fc66f77b6/GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna.gz --refList GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/target_genomes.txt --output GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:05:02,105] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:02,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:05:02,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:05:02,123] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:05:02,123] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 20:05:02,123] [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
--------------------------------------------------------------------------------
[2023-06-08 20:05:02,125] [INFO] DFAST Taxonomy check result was written to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/tc_result.tsv
[2023-06-08 20:05:02,126] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:05:02,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:05:02,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/checkm_data
[2023-06-08 20:05:02,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:05:02,158] [INFO] Task started: CheckM
[2023-06-08 20:05:02,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/checkm_input GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/checkm_result
[2023-06-08 20:05:26,015] [INFO] Task succeeded: CheckM
[2023-06-08 20:05:26,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:05:26,037] [INFO] ===== Completeness check finished =====
[2023-06-08 20:05:26,037] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:05:26,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/markers.fasta)
[2023-06-08 20:05:26,038] [INFO] Task started: Blastn
[2023-06-08 20:05:26,038] [INFO] Running command: blastn -query GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2161cfa-3c37-4a3c-8f64-311b8c2f215f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:05:27,594] [INFO] Task succeeded: Blastn
[2023-06-08 20:05:27,598] [INFO] Selected 10 target genomes.
[2023-06-08 20:05:27,599] [INFO] Target genome list was writen to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:05:27,601] [INFO] Task started: fastANI
[2023-06-08 20:05:27,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1b1b8b9-9a35-493a-881f-ec4fc66f77b6/GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna.gz --refList GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/target_genomes_gtdb.txt --output GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:05:32,312] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:32,324] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:05:32,324] [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_902800005.1	s__UBA1213 sp902800005	100.0	711	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.32	99.32	0.91	0.91	2	conclusive
GCA_900317795.1	s__UBA1213 sp900317795	82.3195	406	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	97.97	97.34	0.76	0.68	10	-
GCA_902801715.1	s__UBA1213 sp902801715	82.1353	335	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002309275.1	s__UBA1213 sp002309275	82.0634	399	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785555.1	s__UBA1213 sp902785555	80.4455	375	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800065.1	s__UBA1213 sp902800065	80.0393	348	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350705.1	s__UBA1213 sp002350705	78.1895	241	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.87	99.87	0.91	0.91	2	-
GCA_902801055.1	s__UBA1213 sp902801055	76.5954	63	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764235.1	s__UBA1213 sp902764235	76.3666	95	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475765.1	s__UBA1213 sp017475765	76.2381	76	717	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:05:32,326] [INFO] GTDB search result was written to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/result_gtdb.tsv
[2023-06-08 20:05:32,327] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:05:32,329] [INFO] DFAST_QC result json was written to GCA_902800005.1_Rumen_uncultured_genome_RUG14527_genomic.fna/dqc_result.json
[2023-06-08 20:05:32,330] [INFO] DFAST_QC completed!
[2023-06-08 20:05:32,330] [INFO] Total running time: 0h0m46s