[2023-06-08 07:02:40,075] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:02:40,078] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:02:40,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference
[2023-06-08 07:02:41,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:02:41,316] [INFO] Task started: Prodigal
[2023-06-08 07:02:41,316] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe25e1d7-db0d-4cf1-8bcb-18fd70b6634f/GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna.gz | prodigal -d GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/cds.fna -a GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:02:43,733] [INFO] Task succeeded: Prodigal
[2023-06-08 07:02:43,734] [INFO] Task started: HMMsearch
[2023-06-08 07:02:43,734] [INFO] Running command: hmmsearch --tblout GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/reference_markers.hmm GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:02:43,996] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:02:43,999] [INFO] Found 6/6 markers.
[2023-06-08 07:02:44,016] [INFO] Query marker FASTA was written to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/markers.fasta
[2023-06-08 07:02:44,016] [INFO] Task started: Blastn
[2023-06-08 07:02:44,016] [INFO] Running command: blastn -query GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/reference_markers.fasta -out GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:02:44,662] [INFO] Task succeeded: Blastn
[2023-06-08 07:02:44,667] [INFO] Selected 29 target genomes.
[2023-06-08 07:02:44,668] [INFO] Target genome list was writen to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/target_genomes.txt
[2023-06-08 07:02:44,677] [INFO] Task started: fastANI
[2023-06-08 07:02:44,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe25e1d7-db0d-4cf1-8bcb-18fd70b6634f/GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna.gz --refList GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/target_genomes.txt --output GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:03:00,072] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:00,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:03:00,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:03:00,075] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:03:00,075] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:03:00,075] [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 07:03:00,077] [INFO] DFAST Taxonomy check result was written to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/tc_result.tsv
[2023-06-08 07:03:00,077] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:03:00,077] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:03:00,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/checkm_data
[2023-06-08 07:03:00,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:03:00,098] [INFO] Task started: CheckM
[2023-06-08 07:03:00,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/checkm_input GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/checkm_result
[2023-06-08 07:03:17,147] [INFO] Task succeeded: CheckM
[2023-06-08 07:03:17,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:03:17,171] [INFO] ===== Completeness check finished =====
[2023-06-08 07:03:17,171] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:03:17,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/markers.fasta)
[2023-06-08 07:03:17,172] [INFO] Task started: Blastn
[2023-06-08 07:03:17,172] [INFO] Running command: blastn -query GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e91b9f-ee2b-4fe7-b5cc-08cb99a4c44f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:03:18,293] [INFO] Task succeeded: Blastn
[2023-06-08 07:03:18,297] [INFO] Selected 12 target genomes.
[2023-06-08 07:03:18,297] [INFO] Target genome list was writen to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:03:18,303] [INFO] Task started: fastANI
[2023-06-08 07:03:18,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe25e1d7-db0d-4cf1-8bcb-18fd70b6634f/GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna.gz --refList GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/target_genomes_gtdb.txt --output GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:03:20,820] [INFO] Task succeeded: fastANI
[2023-06-08 07:03:20,837] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:03:20,837] [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_902774305.1	s__Enterousia sp902774305	100.0	278	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017534945.1	s__Enterousia sp017534945	81.7715	179	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802115.1	s__Enterousia sp902802115	80.6982	166	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	96.53	96.53	0.93	0.93	2	-
GCA_902799285.1	s__Enterousia sp902799285	80.5724	155	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064365.1	s__Enterousia sp018064365	80.4651	156	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793435.1	s__Enterousia sp902793435	80.3275	177	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793005.1	s__Enterousia sp902793005	79.9666	146	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	97.34	97.05	0.93	0.89	4	-
GCA_002371155.1	s__Enterousia sp002371155	79.3107	146	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	95.45	95.45	0.88	0.88	2	-
GCA_002373935.1	s__Enterousia sp002373935	79.0001	153	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781465.1	s__Enterousia sp902781465	78.6333	94	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642585.1	s__Enterousia sp017642585	78.0213	96	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771695.1	s__Enterousia sp902771695	77.911	88	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rs-D84;f__Rs-D84;g__Enterousia	95.0	98.07	98.07	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-08 07:03:20,840] [INFO] GTDB search result was written to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/result_gtdb.tsv
[2023-06-08 07:03:20,841] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:03:20,845] [INFO] DFAST_QC result json was written to GCA_902774305.1_Rumen_uncultured_genome_RUG11963_genomic.fna/dqc_result.json
[2023-06-08 07:03:20,845] [INFO] DFAST_QC completed!
[2023-06-08 07:03:20,845] [INFO] Total running time: 0h0m41s