[2023-06-04 23:12:04,038] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:12:04,044] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:12:04,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference
[2023-06-04 23:12:05,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:12:05,905] [INFO] Task started: Prodigal
[2023-06-04 23:12:05,905] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1c1799c-1281-4a8e-a73f-d564e41fb439/GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna.gz | prodigal -d GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/cds.fna -a GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:12:11,875] [INFO] Task succeeded: Prodigal
[2023-06-04 23:12:11,875] [INFO] Task started: HMMsearch
[2023-06-04 23:12:11,876] [INFO] Running command: hmmsearch --tblout GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/reference_markers.hmm GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:12:12,105] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:12:12,106] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1c1799c-1281-4a8e-a73f-d564e41fb439/GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna.gz]
[2023-06-04 23:12:12,132] [INFO] Query marker FASTA was written to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/markers.fasta
[2023-06-04 23:12:12,133] [INFO] Task started: Blastn
[2023-06-04 23:12:12,133] [INFO] Running command: blastn -query GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/reference_markers.fasta -out GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:12,833] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:12,837] [INFO] Selected 30 target genomes.
[2023-06-04 23:12:12,838] [INFO] Target genome list was writen to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/target_genomes.txt
[2023-06-04 23:12:12,875] [INFO] Task started: fastANI
[2023-06-04 23:12:12,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1c1799c-1281-4a8e-a73f-d564e41fb439/GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna.gz --refList GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/target_genomes.txt --output GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:12:30,479] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:30,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:12:30,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:12:30,489] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:12:30,489] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 23:12:30,489] [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 23:12:30,491] [INFO] DFAST Taxonomy check result was written to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/tc_result.tsv
[2023-06-04 23:12:30,491] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:12:30,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:12:30,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/checkm_data
[2023-06-04 23:12:30,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:12:30,525] [INFO] Task started: CheckM
[2023-06-04 23:12:30,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/checkm_input GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/checkm_result
[2023-06-04 23:12:54,320] [INFO] Task succeeded: CheckM
[2023-06-04 23:12:54,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:12:54,344] [INFO] ===== Completeness check finished =====
[2023-06-04 23:12:54,344] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:12:54,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/markers.fasta)
[2023-06-04 23:12:54,345] [INFO] Task started: Blastn
[2023-06-04 23:12:54,345] [INFO] Running command: blastn -query GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeccc89d-f9a3-4b53-b1de-7b6e82d5494e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:55,442] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:55,447] [INFO] Selected 21 target genomes.
[2023-06-04 23:12:55,447] [INFO] Target genome list was writen to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:12:55,645] [INFO] Task started: fastANI
[2023-06-04 23:12:55,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1c1799c-1281-4a8e-a73f-d564e41fb439/GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna.gz --refList GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/target_genomes_gtdb.txt --output GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:13:07,262] [INFO] Task succeeded: fastANI
[2023-06-04 23:13:07,268] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:13:07,269] [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_002351705.1	s__UBA2810 sp002351705	99.6446	633	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__UBA2810	95.0	99.31	99.12	0.86	0.74	7	conclusive
GCA_900317945.1	s__UBA2810 sp900317945	88.9701	616	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__UBA2810	95.0	98.76	98.04	0.87	0.82	22	-
--------------------------------------------------------------------------------
[2023-06-04 23:13:07,271] [INFO] GTDB search result was written to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/result_gtdb.tsv
[2023-06-04 23:13:07,271] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:13:07,274] [INFO] DFAST_QC result json was written to GCA_902801835.1_Rumen_uncultured_genome_RUG14716_genomic.fna/dqc_result.json
[2023-06-04 23:13:07,274] [INFO] DFAST_QC completed!
[2023-06-04 23:13:07,274] [INFO] Total running time: 0h1m3s