[2023-06-08 13:33:26,931] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:26,933] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:26,933] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference
[2023-06-08 13:33:28,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:28,083] [INFO] Task started: Prodigal
[2023-06-08 13:33:28,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgfab15b5b-2e71-4d39-8725-5fcb7224bdfd/GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna.gz | prodigal -d GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/cds.fna -a GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:33,187] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:33,187] [INFO] Task started: HMMsearch
[2023-06-08 13:33:33,187] [INFO] Running command: hmmsearch --tblout GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/reference_markers.hmm GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:33,369] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:33,370] [INFO] Found 6/6 markers.
[2023-06-08 13:33:33,393] [INFO] Query marker FASTA was written to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/markers.fasta
[2023-06-08 13:33:33,394] [INFO] Task started: Blastn
[2023-06-08 13:33:33,394] [INFO] Running command: blastn -query GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/reference_markers.fasta -out GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:33,996] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:33,999] [INFO] Selected 27 target genomes.
[2023-06-08 13:33:33,999] [INFO] Target genome list was writen to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/target_genomes.txt
[2023-06-08 13:33:34,005] [INFO] Task started: fastANI
[2023-06-08 13:33:34,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab15b5b-2e71-4d39-8725-5fcb7224bdfd/GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna.gz --refList GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/target_genomes.txt --output GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:49,853] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:49,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:49,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:49,855] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:49,855] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:33:49,855] [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 13:33:49,857] [INFO] DFAST Taxonomy check result was written to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/tc_result.tsv
[2023-06-08 13:33:49,857] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:49,858] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:49,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/checkm_data
[2023-06-08 13:33:49,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:49,889] [INFO] Task started: CheckM
[2023-06-08 13:33:49,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/checkm_input GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/checkm_result
[2023-06-08 13:34:09,679] [INFO] Task succeeded: CheckM
[2023-06-08 13:34:09,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:34:09,697] [INFO] ===== Completeness check finished =====
[2023-06-08 13:34:09,698] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:34:09,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/markers.fasta)
[2023-06-08 13:34:09,698] [INFO] Task started: Blastn
[2023-06-08 13:34:09,698] [INFO] Running command: blastn -query GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb88e2e0-a3ce-47c6-bcad-d21b39278f09/dqc_reference/reference_markers_gtdb.fasta -out GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:34:10,776] [INFO] Task succeeded: Blastn
[2023-06-08 13:34:10,779] [INFO] Selected 25 target genomes.
[2023-06-08 13:34:10,779] [INFO] Target genome list was writen to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:34:10,817] [INFO] Task started: fastANI
[2023-06-08 13:34:10,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab15b5b-2e71-4d39-8725-5fcb7224bdfd/GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna.gz --refList GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/target_genomes_gtdb.txt --output GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:34:20,963] [INFO] Task succeeded: fastANI
[2023-06-08 13:34:20,968] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:34:20,968] [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_900313745.1	s__CAG-791 sp900313745	98.177	382	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.33	98.33	0.73	0.73	2	conclusive
GCA_017405805.1	s__CAG-791 sp017405805	77.0929	50	656	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	-
GCF_900625025.1	s__CAG-791 sp900625025	76.9375	60	656	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_902781655.1	s__CAG-791 sp902781655	76.6092	58	656	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_017535945.1	s__Butyrivibrio sp017535945	76.4436	56	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	97.77	97.77	0.82	0.82	2	-
GCA_900320025.1	s__CAG-791 sp900320025	76.4296	53	656	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.86	98.12	0.80	0.73	19	-
--------------------------------------------------------------------------------
[2023-06-08 13:34:20,970] [INFO] GTDB search result was written to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/result_gtdb.tsv
[2023-06-08 13:34:20,970] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:34:20,972] [INFO] DFAST_QC result json was written to GCA_902803445.1_Rumen_uncultured_genome_RUG14877_genomic.fna/dqc_result.json
[2023-06-08 13:34:20,973] [INFO] DFAST_QC completed!
[2023-06-08 13:34:20,973] [INFO] Total running time: 0h0m54s