[2023-06-04 20:54:38,535] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:54:38,538] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:54:38,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference
[2023-06-04 20:54:39,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:54:39,949] [INFO] Task started: Prodigal
[2023-06-04 20:54:39,950] [INFO] Running command: gunzip -c /var/lib/cwl/stga701efc6-cf2e-41ac-995c-015c1355d549/GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna.gz | prodigal -d GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/cds.fna -a GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:54:45,669] [INFO] Task succeeded: Prodigal
[2023-06-04 20:54:45,670] [INFO] Task started: HMMsearch
[2023-06-04 20:54:45,670] [INFO] Running command: hmmsearch --tblout GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/reference_markers.hmm GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:54:45,956] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:54:45,958] [INFO] Found 6/6 markers.
[2023-06-04 20:54:45,994] [INFO] Query marker FASTA was written to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/markers.fasta
[2023-06-04 20:54:45,995] [INFO] Task started: Blastn
[2023-06-04 20:54:45,995] [INFO] Running command: blastn -query GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/markers.fasta -db /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/reference_markers.fasta -out GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:54:46,589] [INFO] Task succeeded: Blastn
[2023-06-04 20:54:46,593] [INFO] Selected 19 target genomes.
[2023-06-04 20:54:46,593] [INFO] Target genome list was writen to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/target_genomes.txt
[2023-06-04 20:54:46,598] [INFO] Task started: fastANI
[2023-06-04 20:54:46,599] [INFO] Running command: fastANI --query /var/lib/cwl/stga701efc6-cf2e-41ac-995c-015c1355d549/GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna.gz --refList GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/target_genomes.txt --output GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:54:58,471] [INFO] Task succeeded: fastANI
[2023-06-04 20:54:58,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:54:58,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:54:58,474] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:54:58,474] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:54:58,474] [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 20:54:58,476] [INFO] DFAST Taxonomy check result was written to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/tc_result.tsv
[2023-06-04 20:54:58,477] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:54:58,477] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:54:58,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/checkm_data
[2023-06-04 20:54:58,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:54:58,509] [INFO] Task started: CheckM
[2023-06-04 20:54:58,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/checkm_input GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/checkm_result
[2023-06-04 20:55:22,536] [INFO] Task succeeded: CheckM
[2023-06-04 20:55:22,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:55:22,558] [INFO] ===== Completeness check finished =====
[2023-06-04 20:55:22,558] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:55:22,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/markers.fasta)
[2023-06-04 20:55:22,559] [INFO] Task started: Blastn
[2023-06-04 20:55:22,559] [INFO] Running command: blastn -query GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/markers.fasta -db /var/lib/cwl/stg897f67c3-89f4-423e-8f96-fb2b3e89fcb0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:55:23,410] [INFO] Task succeeded: Blastn
[2023-06-04 20:55:23,417] [INFO] Selected 17 target genomes.
[2023-06-04 20:55:23,417] [INFO] Target genome list was writen to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:55:23,427] [INFO] Task started: fastANI
[2023-06-04 20:55:23,427] [INFO] Running command: fastANI --query /var/lib/cwl/stga701efc6-cf2e-41ac-995c-015c1355d549/GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna.gz --refList GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/target_genomes_gtdb.txt --output GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:55:31,636] [INFO] Task succeeded: fastANI
[2023-06-04 20:55:31,647] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:55:31,648] [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
GCF_900101015.1	s__CAG-791 sp900101015	98.265	695	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.38	97.83	0.92	0.75	35	conclusive
GCA_902781215.1	s__CAG-791 sp902781215	79.7425	280	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
GCA_900321785.1	s__CAG-791 sp900321785	79.5522	201	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.92	97.67	0.83	0.75	9	-
GCA_017513005.1	s__CAG-791 sp017513005	79.3829	252	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.02	99.02	0.89	0.89	2	-
GCA_902780385.1	s__CAG-791 sp902780385	79.349	284	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.16	97.16	0.72	0.72	2	-
GCA_900318375.1	s__CAG-791 sp900318375	79.1945	260	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.93	99.93	0.92	0.92	2	-
GCA_002394525.1	s__CAG-791 sp002394525	79.1313	209	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.96	97.96	0.79	0.79	2	-
GCA_002390025.1	s__CAG-791 sp002390025	78.917	248	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002358875.1	s__CAG-791 sp002358875	78.8936	204	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405805.1	s__CAG-791 sp017405805	77.7375	107	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469935.1	s__CAG-791 sp017469935	77.5665	113	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319245.1	s__CAG-791 sp900319245	77.4155	107	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.27	97.33	0.84	0.77	7	-
GCA_902801585.1	s__CAG-791 sp902801585	77.3165	104	730	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:55:31,650] [INFO] GTDB search result was written to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/result_gtdb.tsv
[2023-06-04 20:55:31,651] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:55:31,655] [INFO] DFAST_QC result json was written to GCA_902792525.1_Rumen_uncultured_genome_RUG13773_genomic.fna/dqc_result.json
[2023-06-04 20:55:31,655] [INFO] DFAST_QC completed!
[2023-06-04 20:55:31,656] [INFO] Total running time: 0h0m53s