[2023-06-04 17:34:39,432] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:34:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:34:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference
[2023-06-04 17:34:40,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:34:40,699] [INFO] Task started: Prodigal
[2023-06-04 17:34:40,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgec75604a-fb95-4c27-80ad-53335da0416e/GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna.gz | prodigal -d GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/cds.fna -a GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:34:53,904] [INFO] Task succeeded: Prodigal
[2023-06-04 17:34:53,905] [INFO] Task started: HMMsearch
[2023-06-04 17:34:53,905] [INFO] Running command: hmmsearch --tblout GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/reference_markers.hmm GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:34:54,161] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:34:54,163] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgec75604a-fb95-4c27-80ad-53335da0416e/GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna.gz]
[2023-06-04 17:34:54,188] [INFO] Query marker FASTA was written to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/markers.fasta
[2023-06-04 17:34:54,189] [INFO] Task started: Blastn
[2023-06-04 17:34:54,189] [INFO] Running command: blastn -query GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/reference_markers.fasta -out GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:34:54,783] [INFO] Task succeeded: Blastn
[2023-06-04 17:34:54,788] [INFO] Selected 31 target genomes.
[2023-06-04 17:34:54,788] [INFO] Target genome list was writen to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/target_genomes.txt
[2023-06-04 17:34:54,851] [INFO] Task started: fastANI
[2023-06-04 17:34:54,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgec75604a-fb95-4c27-80ad-53335da0416e/GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna.gz --refList GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/target_genomes.txt --output GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:35:12,710] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:12,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:35:12,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:35:12,724] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:35:12,724] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:35:12,724] [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
--------------------------------------------------------------------------------
[2023-06-04 17:35:12,727] [INFO] DFAST Taxonomy check result was written to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/tc_result.tsv
[2023-06-04 17:35:12,727] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:35:12,728] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:35:12,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/checkm_data
[2023-06-04 17:35:12,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:35:12,761] [INFO] Task started: CheckM
[2023-06-04 17:35:12,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/checkm_input GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/checkm_result
[2023-06-04 17:35:53,252] [INFO] Task succeeded: CheckM
[2023-06-04 17:35:53,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.37%
Contamintation: 10.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:35:53,278] [INFO] ===== Completeness check finished =====
[2023-06-04 17:35:53,278] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:35:53,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/markers.fasta)
[2023-06-04 17:35:53,279] [INFO] Task started: Blastn
[2023-06-04 17:35:53,279] [INFO] Running command: blastn -query GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f47dbbf-84d8-4908-a0e3-22e9fccff9a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:54,211] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:54,230] [INFO] Selected 19 target genomes.
[2023-06-04 17:35:54,230] [INFO] Target genome list was writen to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:35:54,384] [INFO] Task started: fastANI
[2023-06-04 17:35:54,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgec75604a-fb95-4c27-80ad-53335da0416e/GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna.gz --refList GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/target_genomes_gtdb.txt --output GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:36:05,383] [INFO] Task succeeded: fastANI
[2023-06-04 17:36:05,398] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:36:05,398] [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_900319925.1	s__F23-D06 sp900319925	96.8912	424	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	97.32	96.04	0.81	0.73	14	conclusive
GCA_902770735.1	s__F23-D06 sp902770735	84.9144	332	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	97.49	97.03	0.76	0.71	3	-
GCA_017395245.1	s__F23-D06 sp017395245	84.3845	385	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235135.1	s__F23-D06 sp905235135	83.373	366	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	97.20	97.20	0.77	0.77	2	-
GCA_017962275.1	s__F23-D06 sp017962275	83.0647	334	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527945.1	s__F23-D06 sp017527945	82.8764	319	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316305.1	s__F23-D06 sp900316305	82.3	330	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	98.90	98.28	0.91	0.85	4	-
GCA_900317715.1	s__F23-D06 sp900317715	81.6485	291	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016281255.1	s__F23-D06 sp016281255	81.5205	280	533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__F23-D06	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:36:05,400] [INFO] GTDB search result was written to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/result_gtdb.tsv
[2023-06-04 17:36:05,401] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:36:05,404] [INFO] DFAST_QC result json was written to GCA_902770035.1_Rumen_uncultured_genome_RUG11535_genomic.fna/dqc_result.json
[2023-06-04 17:36:05,404] [INFO] DFAST_QC completed!
[2023-06-04 17:36:05,404] [INFO] Total running time: 0h1m26s