[2023-06-04 17:57:28,806] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:57:28,809] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:57:28,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference
[2023-06-04 17:57:31,177] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:57:31,179] [INFO] Task started: Prodigal
[2023-06-04 17:57:31,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg289fb3fa-131b-4eb0-8e59-31646688a5e3/GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna.gz | prodigal -d GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/cds.fna -a GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:57:35,917] [INFO] Task succeeded: Prodigal
[2023-06-04 17:57:35,917] [INFO] Task started: HMMsearch
[2023-06-04 17:57:35,918] [INFO] Running command: hmmsearch --tblout GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/reference_markers.hmm GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:57:36,151] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:57:36,153] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg289fb3fa-131b-4eb0-8e59-31646688a5e3/GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna.gz]
[2023-06-04 17:57:36,182] [INFO] Query marker FASTA was written to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/markers.fasta
[2023-06-04 17:57:36,183] [INFO] Task started: Blastn
[2023-06-04 17:57:36,183] [INFO] Running command: blastn -query GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/markers.fasta -db /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/reference_markers.fasta -out GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:57:36,782] [INFO] Task succeeded: Blastn
[2023-06-04 17:57:36,786] [INFO] Selected 16 target genomes.
[2023-06-04 17:57:36,787] [INFO] Target genome list was writen to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/target_genomes.txt
[2023-06-04 17:57:37,465] [INFO] Task started: fastANI
[2023-06-04 17:57:37,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg289fb3fa-131b-4eb0-8e59-31646688a5e3/GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna.gz --refList GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/target_genomes.txt --output GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:57:46,395] [INFO] Task succeeded: fastANI
[2023-06-04 17:57:46,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:57:46,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:57:46,399] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:57:46,399] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:57:46,400] [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 17:57:46,402] [INFO] DFAST Taxonomy check result was written to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/tc_result.tsv
[2023-06-04 17:57:46,403] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:57:46,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:57:46,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/checkm_data
[2023-06-04 17:57:46,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:57:46,434] [INFO] Task started: CheckM
[2023-06-04 17:57:46,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/checkm_input GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/checkm_result
[2023-06-04 17:58:07,826] [INFO] Task succeeded: CheckM
[2023-06-04 17:58:07,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.25%
Contamintation: 10.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:58:07,851] [INFO] ===== Completeness check finished =====
[2023-06-04 17:58:07,851] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:58:07,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/markers.fasta)
[2023-06-04 17:58:07,852] [INFO] Task started: Blastn
[2023-06-04 17:58:07,852] [INFO] Running command: blastn -query GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/markers.fasta -db /var/lib/cwl/stg13d7d8e5-9aa5-4cb7-92b1-8772169921b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:08,757] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:08,761] [INFO] Selected 11 target genomes.
[2023-06-04 17:58:08,762] [INFO] Target genome list was writen to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:58:09,074] [INFO] Task started: fastANI
[2023-06-04 17:58:09,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg289fb3fa-131b-4eb0-8e59-31646688a5e3/GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna.gz --refList GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/target_genomes_gtdb.txt --output GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:58:13,572] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:13,583] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:58:13,583] [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_902782875.1	s__CAG-353 sp902782875	99.9999	512	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018110925.1	s__CAG-353 sp018110925	81.255	240	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410745.1	s__CAG-353 sp017410745	79.1268	165	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468865.1	s__CAG-353 sp017468865	77.7358	107	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017394475.1	s__CAG-353 sp017394475	77.3204	80	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363145.1	s__CAG-353 sp900066885	77.1304	76	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	98.51	98.32	0.91	0.87	6	-
GCA_017544185.1	s__CAG-353 sp017544185	76.8559	81	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110985.1	s__CAG-353 sp018110985	76.7739	77	527	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:58:13,585] [INFO] GTDB search result was written to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/result_gtdb.tsv
[2023-06-04 17:58:13,586] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:58:13,589] [INFO] DFAST_QC result json was written to GCA_902782875.1_Rumen_uncultured_genome_RUG12814_genomic.fna/dqc_result.json
[2023-06-04 17:58:13,589] [INFO] DFAST_QC completed!
[2023-06-04 17:58:13,589] [INFO] Total running time: 0h0m45s