[2023-06-05 03:59:54,841] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:59:54,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:59:54,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference
[2023-06-05 03:59:56,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:59:56,129] [INFO] Task started: Prodigal
[2023-06-05 03:59:56,129] [INFO] Running command: gunzip -c /var/lib/cwl/stgb038d284-1055-4825-9225-a9dbeefe8176/GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna.gz | prodigal -d GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/cds.fna -a GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:00:15,829] [INFO] Task succeeded: Prodigal
[2023-06-05 04:00:15,830] [INFO] Task started: HMMsearch
[2023-06-05 04:00:15,830] [INFO] Running command: hmmsearch --tblout GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/reference_markers.hmm GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:00:16,084] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:00:16,086] [INFO] Found 6/6 markers.
[2023-06-05 04:00:16,119] [INFO] Query marker FASTA was written to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/markers.fasta
[2023-06-05 04:00:16,120] [INFO] Task started: Blastn
[2023-06-05 04:00:16,120] [INFO] Running command: blastn -query GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/reference_markers.fasta -out GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:00:16,715] [INFO] Task succeeded: Blastn
[2023-06-05 04:00:16,719] [INFO] Selected 31 target genomes.
[2023-06-05 04:00:16,719] [INFO] Target genome list was writen to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/target_genomes.txt
[2023-06-05 04:00:16,722] [INFO] Task started: fastANI
[2023-06-05 04:00:16,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgb038d284-1055-4825-9225-a9dbeefe8176/GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna.gz --refList GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/target_genomes.txt --output GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:00:31,371] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:31,372] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:00:31,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:00:31,378] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:00:31,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:00:31,378] [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
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.7985	103	945	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:00:31,380] [INFO] DFAST Taxonomy check result was written to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/tc_result.tsv
[2023-06-05 04:00:31,381] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:00:31,381] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:00:31,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/checkm_data
[2023-06-05 04:00:31,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:00:31,416] [INFO] Task started: CheckM
[2023-06-05 04:00:31,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/checkm_input GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/checkm_result
[2023-06-05 04:01:30,279] [INFO] Task succeeded: CheckM
[2023-06-05 04:01:30,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:01:30,302] [INFO] ===== Completeness check finished =====
[2023-06-05 04:01:30,302] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:01:30,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/markers.fasta)
[2023-06-05 04:01:30,303] [INFO] Task started: Blastn
[2023-06-05 04:01:30,303] [INFO] Running command: blastn -query GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cb0e9ca-a6f0-471e-8cc5-f78478ad1aac/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:01:31,139] [INFO] Task succeeded: Blastn
[2023-06-05 04:01:31,144] [INFO] Selected 11 target genomes.
[2023-06-05 04:01:31,144] [INFO] Target genome list was writen to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:01:31,147] [INFO] Task started: fastANI
[2023-06-05 04:01:31,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgb038d284-1055-4825-9225-a9dbeefe8176/GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna.gz --refList GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/target_genomes_gtdb.txt --output GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:01:37,627] [INFO] Task succeeded: fastANI
[2023-06-05 04:01:37,647] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:01:37,648] [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
GCA_902801475.1	s__UBA4334 sp902801475	97.5288	771	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.71	97.36	0.83	0.79	15	conclusive
GCA_017614895.1	s__UBA4334 sp017614895	85.1778	562	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534815.1	s__UBA4334 sp017534815	83.4103	472	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768125.1	s__UBA4334 sp902768125	83.0234	567	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.29	98.29	0.89	0.89	2	-
GCA_017651245.1	s__UBA4334 sp017651245	82.5052	565	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316505.1	s__UBA4334 sp900316505	82.1704	566	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.97	97.14	0.89	0.83	54	-
GCA_905234125.1	s__UBA4334 sp905234125	81.5667	463	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
GCA_902803605.1	s__UBA4334 sp902803605	81.2632	394	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617805.1	s__UBA4334 sp017617805	81.0572	348	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280445.1	s__UBA4334 sp016280445	80.559	454	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483605.1	s__UBA4334 sp017483605	79.7076	362	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.79	96.79	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-05 04:01:37,650] [INFO] GTDB search result was written to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/result_gtdb.tsv
[2023-06-05 04:01:37,651] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:01:37,656] [INFO] DFAST_QC result json was written to GCA_902784875.1_Rumen_uncultured_genome_RUG13019_genomic.fna/dqc_result.json
[2023-06-05 04:01:37,657] [INFO] DFAST_QC completed!
[2023-06-05 04:01:37,657] [INFO] Total running time: 0h1m43s