[2023-06-04 21:50:06,046] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:50:06,049] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:50:06,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference
[2023-06-04 21:50:08,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:50:08,333] [INFO] Task started: Prodigal
[2023-06-04 21:50:08,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg402cd8d6-5756-4994-91e4-2a36bf8ae1e7/GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna.gz | prodigal -d GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/cds.fna -a GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:50:10,687] [INFO] Task succeeded: Prodigal
[2023-06-04 21:50:10,687] [INFO] Task started: HMMsearch
[2023-06-04 21:50:10,688] [INFO] Running command: hmmsearch --tblout GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/reference_markers.hmm GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:50:10,902] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:50:10,903] [INFO] Found 6/6 markers.
[2023-06-04 21:50:10,918] [INFO] Query marker FASTA was written to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/markers.fasta
[2023-06-04 21:50:10,918] [INFO] Task started: Blastn
[2023-06-04 21:50:10,918] [INFO] Running command: blastn -query GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/markers.fasta -db /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/reference_markers.fasta -out GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:50:12,217] [INFO] Task succeeded: Blastn
[2023-06-04 21:50:12,221] [INFO] Selected 13 target genomes.
[2023-06-04 21:50:12,222] [INFO] Target genome list was writen to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/target_genomes.txt
[2023-06-04 21:50:12,236] [INFO] Task started: fastANI
[2023-06-04 21:50:12,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg402cd8d6-5756-4994-91e4-2a36bf8ae1e7/GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna.gz --refList GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/target_genomes.txt --output GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:50:17,854] [INFO] Task succeeded: fastANI
[2023-06-04 21:50:17,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:50:17,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:50:17,857] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:50:17,857] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:50:17,858] [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 21:50:17,860] [INFO] DFAST Taxonomy check result was written to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/tc_result.tsv
[2023-06-04 21:50:17,861] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:50:17,861] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:50:17,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/checkm_data
[2023-06-04 21:50:17,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:50:17,882] [INFO] Task started: CheckM
[2023-06-04 21:50:17,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/checkm_input GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/checkm_result
[2023-06-04 21:50:32,832] [INFO] Task succeeded: CheckM
[2023-06-04 21:50:32,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:50:32,853] [INFO] ===== Completeness check finished =====
[2023-06-04 21:50:32,853] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:50:32,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/markers.fasta)
[2023-06-04 21:50:32,854] [INFO] Task started: Blastn
[2023-06-04 21:50:32,854] [INFO] Running command: blastn -query GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/markers.fasta -db /var/lib/cwl/stg562252ed-b4be-4757-b747-fa3b8ac85779/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:50:33,675] [INFO] Task succeeded: Blastn
[2023-06-04 21:50:33,680] [INFO] Selected 6 target genomes.
[2023-06-04 21:50:33,680] [INFO] Target genome list was writen to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:50:33,684] [INFO] Task started: fastANI
[2023-06-04 21:50:33,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg402cd8d6-5756-4994-91e4-2a36bf8ae1e7/GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna.gz --refList GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/target_genomes_gtdb.txt --output GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:50:35,080] [INFO] Task succeeded: fastANI
[2023-06-04 21:50:35,087] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:50:35,087] [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_902771535.1	s__UBA3830 sp902771535	100.0	324	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	98.37	98.29	0.91	0.86	4	conclusive
GCA_902761495.1	s__UBA3830 sp902761495	92.3012	252	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017649895.1	s__UBA3830 sp017649895	90.5632	287	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790255.1	s__UBA3830 sp902790255	82.7004	203	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017614525.1	s__UBA3830 sp017614525	80.5637	166	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002393025.1	s__UBA3830 sp002393025	79.5357	140	327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA3830;f__UBA3830;g__UBA3830	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:50:35,089] [INFO] GTDB search result was written to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/result_gtdb.tsv
[2023-06-04 21:50:35,090] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:50:35,092] [INFO] DFAST_QC result json was written to GCA_902771535.1_Rumen_uncultured_genome_RUG11675_genomic.fna/dqc_result.json
[2023-06-04 21:50:35,092] [INFO] DFAST_QC completed!
[2023-06-04 21:50:35,092] [INFO] Total running time: 0h0m29s