[2023-06-08 12:27:15,194] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:27:15,197] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:27:15,197] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference
[2023-06-08 12:27:16,715] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:27:16,716] [INFO] Task started: Prodigal
[2023-06-08 12:27:16,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3344c3a-c222-47a1-a8d2-614d67f7196f/GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna.gz | prodigal -d GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/cds.fna -a GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:27:18,729] [INFO] Task succeeded: Prodigal
[2023-06-08 12:27:18,729] [INFO] Task started: HMMsearch
[2023-06-08 12:27:18,730] [INFO] Running command: hmmsearch --tblout GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/reference_markers.hmm GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:27:18,959] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:27:18,960] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3344c3a-c222-47a1-a8d2-614d67f7196f/GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna.gz]
[2023-06-08 12:27:18,981] [INFO] Query marker FASTA was written to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/markers.fasta
[2023-06-08 12:27:18,981] [INFO] Task started: Blastn
[2023-06-08 12:27:18,981] [INFO] Running command: blastn -query GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/reference_markers.fasta -out GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:21,058] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:21,062] [INFO] Selected 20 target genomes.
[2023-06-08 12:27:21,063] [INFO] Target genome list was writen to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/target_genomes.txt
[2023-06-08 12:27:21,092] [INFO] Task started: fastANI
[2023-06-08 12:27:21,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3344c3a-c222-47a1-a8d2-614d67f7196f/GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna.gz --refList GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/target_genomes.txt --output GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:26,857] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:26,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:26,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:26,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:26,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:27:26,860] [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 12:27:26,863] [INFO] DFAST Taxonomy check result was written to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/tc_result.tsv
[2023-06-08 12:27:26,864] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:26,864] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:26,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/checkm_data
[2023-06-08 12:27:26,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:26,884] [INFO] Task started: CheckM
[2023-06-08 12:27:26,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/checkm_input GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/checkm_result
[2023-06-08 12:27:45,098] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:45,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:45,120] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:45,121] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:45,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/markers.fasta)
[2023-06-08 12:27:45,122] [INFO] Task started: Blastn
[2023-06-08 12:27:45,122] [INFO] Running command: blastn -query GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0746bea-c419-4279-80b1-ffa772601fa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:45,911] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:45,916] [INFO] Selected 19 target genomes.
[2023-06-08 12:27:45,916] [INFO] Target genome list was writen to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:45,921] [INFO] Task started: fastANI
[2023-06-08 12:27:45,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3344c3a-c222-47a1-a8d2-614d67f7196f/GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna.gz --refList GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/target_genomes_gtdb.txt --output GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:50,367] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:50,376] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:27:50,376] [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_902768335.1	s__UBA3207 sp902768335	95.9401	269	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	95.94	95.94	0.84	0.84	2	conclusive
GCA_900314585.1	s__UBA3207 sp900314585	79.9834	172	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	98.34	96.67	0.96	0.93	3	-
GCA_902796125.1	s__UBA3207 sp902796125	77.8335	79	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002363735.1	s__UBA3207 sp002363735	77.8018	56	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797855.1	s__UBA3207 sp902797855	77.3848	70	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447725.1	s__UBA3207 sp017447725	77.186	66	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	97.62	97.37	0.76	0.69	3	-
GCA_018064745.1	s__UBA3207 sp018064745	77.1185	56	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787955.1	s__UBA3207 sp902787955	76.9621	65	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	95.98	95.98	0.91	0.91	2	-
GCA_002395065.1	s__UBA3207 sp002395065	76.7925	56	335	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	96.29	96.29	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:50,378] [INFO] GTDB search result was written to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:50,379] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:50,383] [INFO] DFAST_QC result json was written to GCA_902795575.1_Rumen_uncultured_genome_RUG14084_genomic.fna/dqc_result.json
[2023-06-08 12:27:50,383] [INFO] DFAST_QC completed!
[2023-06-08 12:27:50,384] [INFO] Total running time: 0h0m35s