[2023-06-08 18:25:03,836] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:25:03,838] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:25:03,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference
[2023-06-08 18:25:05,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:25:05,157] [INFO] Task started: Prodigal
[2023-06-08 18:25:05,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg724e38e7-c1b9-4307-b475-27f4f6895b52/GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna.gz | prodigal -d GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/cds.fna -a GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:25:08,629] [INFO] Task succeeded: Prodigal
[2023-06-08 18:25:08,629] [INFO] Task started: HMMsearch
[2023-06-08 18:25:08,630] [INFO] Running command: hmmsearch --tblout GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/reference_markers.hmm GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:25:08,884] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:25:08,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg724e38e7-c1b9-4307-b475-27f4f6895b52/GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna.gz]
[2023-06-08 18:25:08,904] [INFO] Query marker FASTA was written to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/markers.fasta
[2023-06-08 18:25:08,904] [INFO] Task started: Blastn
[2023-06-08 18:25:08,905] [INFO] Running command: blastn -query GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/reference_markers.fasta -out GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:09,545] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:09,549] [INFO] Selected 17 target genomes.
[2023-06-08 18:25:09,549] [INFO] Target genome list was writen to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/target_genomes.txt
[2023-06-08 18:25:09,554] [INFO] Task started: fastANI
[2023-06-08 18:25:09,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg724e38e7-c1b9-4307-b475-27f4f6895b52/GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna.gz --refList GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/target_genomes.txt --output GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:25:20,596] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:20,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:25:20,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:25:20,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:25:20,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 18:25:20,599] [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 18:25:20,601] [INFO] DFAST Taxonomy check result was written to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/tc_result.tsv
[2023-06-08 18:25:20,601] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:25:20,602] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:25:20,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/checkm_data
[2023-06-08 18:25:20,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:25:20,627] [INFO] Task started: CheckM
[2023-06-08 18:25:20,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/checkm_input GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/checkm_result
[2023-06-08 18:25:39,570] [INFO] Task succeeded: CheckM
[2023-06-08 18:25:39,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 12.50%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-08 18:25:39,599] [INFO] ===== Completeness check finished =====
[2023-06-08 18:25:39,599] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:25:39,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/markers.fasta)
[2023-06-08 18:25:39,600] [INFO] Task started: Blastn
[2023-06-08 18:25:39,600] [INFO] Running command: blastn -query GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a34007d-07bd-4fc6-8a7a-7b27a9df760d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:40,558] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:40,562] [INFO] Selected 17 target genomes.
[2023-06-08 18:25:40,562] [INFO] Target genome list was writen to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:25:40,573] [INFO] Task started: fastANI
[2023-06-08 18:25:40,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg724e38e7-c1b9-4307-b475-27f4f6895b52/GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna.gz --refList GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/target_genomes_gtdb.txt --output GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:25:47,504] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:47,513] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:25:47,514] [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_902794835.1	s__UBA4951 sp900320745	98.2471	313	426	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	98.52	98.25	0.81	0.75	5	conclusive
GCA_902791935.1	s__UBA4951 sp900321485	86.7016	94	426	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	98.52	97.71	0.90	0.85	4	-
GCA_902791085.1	s__UBA4951 sp902791085	80.3271	51	426	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540385.1	s__UBA4951 sp900540385	78.2425	66	426	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	98.54	97.08	0.92	0.84	3	-
GCA_002297365.1	s__UBA4951 sp002297365	78.0763	74	426	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	99.50	99.37	0.93	0.86	5	-
--------------------------------------------------------------------------------
[2023-06-08 18:25:47,516] [INFO] GTDB search result was written to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/result_gtdb.tsv
[2023-06-08 18:25:47,516] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:25:47,519] [INFO] DFAST_QC result json was written to GCA_902763255.1_Rumen_uncultured_genome_RUG10839_genomic.fna/dqc_result.json
[2023-06-08 18:25:47,519] [INFO] DFAST_QC completed!
[2023-06-08 18:25:47,520] [INFO] Total running time: 0h0m44s