[2023-06-05 00:37:53,606] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:37:53,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:37:53,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference
[2023-06-05 00:37:54,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:37:54,974] [INFO] Task started: Prodigal
[2023-06-05 00:37:54,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48caa93-d856-4049-9c12-84dabacaf753/GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna.gz | prodigal -d GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/cds.fna -a GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:02,458] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:02,459] [INFO] Task started: HMMsearch
[2023-06-05 00:38:02,459] [INFO] Running command: hmmsearch --tblout GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/reference_markers.hmm GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:02,723] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:02,725] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb48caa93-d856-4049-9c12-84dabacaf753/GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna.gz]
[2023-06-05 00:38:02,749] [INFO] Query marker FASTA was written to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/markers.fasta
[2023-06-05 00:38:02,749] [INFO] Task started: Blastn
[2023-06-05 00:38:02,750] [INFO] Running command: blastn -query GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/markers.fasta -db /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/reference_markers.fasta -out GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:03,353] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:03,357] [INFO] Selected 22 target genomes.
[2023-06-05 00:38:03,358] [INFO] Target genome list was writen to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/target_genomes.txt
[2023-06-05 00:38:03,363] [INFO] Task started: fastANI
[2023-06-05 00:38:03,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48caa93-d856-4049-9c12-84dabacaf753/GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna.gz --refList GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/target_genomes.txt --output GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:18,305] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:18,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:18,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:18,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:18,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:38:18,308] [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
--------------------------------------------------------------------------------
[2023-06-05 00:38:18,309] [INFO] DFAST Taxonomy check result was written to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/tc_result.tsv
[2023-06-05 00:38:18,310] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:18,310] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:18,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/checkm_data
[2023-06-05 00:38:18,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:18,337] [INFO] Task started: CheckM
[2023-06-05 00:38:18,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/checkm_input GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/checkm_result
[2023-06-05 00:38:45,064] [INFO] Task succeeded: CheckM
[2023-06-05 00:38:45,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 00:38:45,090] [INFO] ===== Completeness check finished =====
[2023-06-05 00:38:45,090] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:38:45,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/markers.fasta)
[2023-06-05 00:38:45,091] [INFO] Task started: Blastn
[2023-06-05 00:38:45,091] [INFO] Running command: blastn -query GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/markers.fasta -db /var/lib/cwl/stg1428cf4e-d4d8-466f-ba1e-e3a4929c9767/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:46,006] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:46,010] [INFO] Selected 20 target genomes.
[2023-06-05 00:38:46,011] [INFO] Target genome list was writen to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:38:46,178] [INFO] Task started: fastANI
[2023-06-05 00:38:46,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48caa93-d856-4049-9c12-84dabacaf753/GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna.gz --refList GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/target_genomes_gtdb.txt --output GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:38:52,467] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:52,479] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:38:52,480] [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_902797895.1	s__Egerieousia sp902797895	99.9999	437	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	96.60	96.60	0.77	0.77	2	conclusive
GCA_017618115.1	s__Egerieousia sp017618115	77.3745	101	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017959005.1	s__Egerieousia sp017959005	77.2725	99	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554305.1	s__Egerieousia sp017554305	77.2608	107	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.32	97.32	0.92	0.92	2	-
GCA_902769525.1	s__Egerieousia sp902769525	77.0518	58	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.50	96.68	0.91	0.90	5	-
GCA_900322025.1	s__Egerieousia sp900322025	76.826	57	441	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 00:38:52,482] [INFO] GTDB search result was written to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/result_gtdb.tsv
[2023-06-05 00:38:52,482] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:38:52,485] [INFO] DFAST_QC result json was written to GCA_902797895.1_Rumen_uncultured_genome_RUG14315_genomic.fna/dqc_result.json
[2023-06-05 00:38:52,485] [INFO] DFAST_QC completed!
[2023-06-05 00:38:52,485] [INFO] Total running time: 0h0m59s