[2023-06-04 19:38:15,628] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:38:15,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:38:15,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference
[2023-06-04 19:38:16,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:38:16,881] [INFO] Task started: Prodigal
[2023-06-04 19:38:16,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a99705f-498c-4305-893e-7a1470815cba/GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna.gz | prodigal -d GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/cds.fna -a GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:21,481] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:21,481] [INFO] Task started: HMMsearch
[2023-06-04 19:38:21,482] [INFO] Running command: hmmsearch --tblout GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/reference_markers.hmm GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:21,715] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:21,716] [INFO] Found 6/6 markers.
[2023-06-04 19:38:21,736] [INFO] Query marker FASTA was written to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/markers.fasta
[2023-06-04 19:38:21,737] [INFO] Task started: Blastn
[2023-06-04 19:38:21,737] [INFO] Running command: blastn -query GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/markers.fasta -db /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/reference_markers.fasta -out GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:22,581] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:22,587] [INFO] Selected 26 target genomes.
[2023-06-04 19:38:22,587] [INFO] Target genome list was writen to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/target_genomes.txt
[2023-06-04 19:38:22,616] [INFO] Task started: fastANI
[2023-06-04 19:38:22,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a99705f-498c-4305-893e-7a1470815cba/GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna.gz --refList GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/target_genomes.txt --output GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:39,974] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:39,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:39,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:39,978] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:39,978] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:38:39,979] [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 19:38:39,983] [INFO] DFAST Taxonomy check result was written to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/tc_result.tsv
[2023-06-04 19:38:39,984] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:39,984] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:39,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/checkm_data
[2023-06-04 19:38:39,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:40,016] [INFO] Task started: CheckM
[2023-06-04 19:38:40,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/checkm_input GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/checkm_result
[2023-06-04 19:38:59,731] [INFO] Task succeeded: CheckM
[2023-06-04 19:38:59,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.87%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:38:59,754] [INFO] ===== Completeness check finished =====
[2023-06-04 19:38:59,754] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:38:59,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/markers.fasta)
[2023-06-04 19:38:59,755] [INFO] Task started: Blastn
[2023-06-04 19:38:59,755] [INFO] Running command: blastn -query GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/markers.fasta -db /var/lib/cwl/stg274b2a79-d069-404d-91e3-1fe3469bf9d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:39:00,649] [INFO] Task succeeded: Blastn
[2023-06-04 19:39:00,654] [INFO] Selected 10 target genomes.
[2023-06-04 19:39:00,655] [INFO] Target genome list was writen to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:39:00,662] [INFO] Task started: fastANI
[2023-06-04 19:39:00,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a99705f-498c-4305-893e-7a1470815cba/GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna.gz --refList GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/target_genomes_gtdb.txt --output GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:39:05,198] [INFO] Task succeeded: fastANI
[2023-06-04 19:39:05,210] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:39:05,210] [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_902768995.1	s__RUG472 sp902768995	98.319	348	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.42	98.10	0.83	0.75	15	conclusive
GCA_900319345.1	s__RUG472 sp900319345	94.8203	393	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.47	97.84	0.91	0.80	6	-
GCA_902786465.1	s__RUG472 sp902786465	93.7894	359	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.79	0.84	0.84	2	-
GCA_902761365.1	s__RUG472 sp902761365	87.3838	362	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802805.1	s__RUG472 sp902802805	86.9794	345	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.22	97.22	0.86	0.86	2	-
GCA_902801845.1	s__RUG472 sp902801845	86.8588	397	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.35	0.92	0.91	4	-
GCA_902802575.1	s__RUG472 sp902802575	86.55	360	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	95.40	95.40	0.82	0.82	2	-
GCA_017545535.1	s__RUG472 sp017545535	86.2263	388	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798825.1	s__RUG472 sp902798825	86.0875	373	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.85	97.83	0.89	0.89	3	-
GCA_902765005.1	s__RUG472 sp902765005	85.4255	380	477	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:39:05,212] [INFO] GTDB search result was written to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/result_gtdb.tsv
[2023-06-04 19:39:05,213] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:39:05,216] [INFO] DFAST_QC result json was written to GCA_902792455.1_Rumen_uncultured_genome_RUG13780_genomic.fna/dqc_result.json
[2023-06-04 19:39:05,216] [INFO] DFAST_QC completed!
[2023-06-04 19:39:05,216] [INFO] Total running time: 0h0m50s