[2023-06-08 17:09:18,621] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:18,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:18,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference
[2023-06-08 17:09:20,048] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:20,049] [INFO] Task started: Prodigal
[2023-06-08 17:09:20,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg24424757-c3cb-452c-b20c-78d0e3ee44ce/GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna.gz | prodigal -d GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/cds.fna -a GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:26,362] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:26,362] [INFO] Task started: HMMsearch
[2023-06-08 17:09:26,363] [INFO] Running command: hmmsearch --tblout GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/reference_markers.hmm GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:26,607] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:26,609] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg24424757-c3cb-452c-b20c-78d0e3ee44ce/GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna.gz]
[2023-06-08 17:09:26,636] [INFO] Query marker FASTA was written to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/markers.fasta
[2023-06-08 17:09:26,637] [INFO] Task started: Blastn
[2023-06-08 17:09:26,637] [INFO] Running command: blastn -query GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/markers.fasta -db /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/reference_markers.fasta -out GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:27,238] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:27,241] [INFO] Selected 25 target genomes.
[2023-06-08 17:09:27,242] [INFO] Target genome list was writen to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/target_genomes.txt
[2023-06-08 17:09:27,271] [INFO] Task started: fastANI
[2023-06-08 17:09:27,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg24424757-c3cb-452c-b20c-78d0e3ee44ce/GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna.gz --refList GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/target_genomes.txt --output GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:42,487] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:42,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:42,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:42,493] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:42,493] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:09:42,494] [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
Galactobacillus timonensis	strain=Marseille-P4641	GCA_900240265.1	2041840	2041840	type	True	78.275	148	780	95	below_threshold
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	77.1978	100	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:42,496] [INFO] DFAST Taxonomy check result was written to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/tc_result.tsv
[2023-06-08 17:09:42,496] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:42,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:42,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/checkm_data
[2023-06-08 17:09:42,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:42,533] [INFO] Task started: CheckM
[2023-06-08 17:09:42,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/checkm_input GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/checkm_result
[2023-06-08 17:10:08,674] [INFO] Task succeeded: CheckM
[2023-06-08 17:10:08,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:10:08,698] [INFO] ===== Completeness check finished =====
[2023-06-08 17:10:08,698] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:10:08,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/markers.fasta)
[2023-06-08 17:10:08,699] [INFO] Task started: Blastn
[2023-06-08 17:10:08,699] [INFO] Running command: blastn -query GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/markers.fasta -db /var/lib/cwl/stgc749150d-ed03-4fd5-9273-0d3562cd00ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:10:09,546] [INFO] Task succeeded: Blastn
[2023-06-08 17:10:09,551] [INFO] Selected 15 target genomes.
[2023-06-08 17:10:09,551] [INFO] Target genome list was writen to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:10:09,559] [INFO] Task started: fastANI
[2023-06-08 17:10:09,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg24424757-c3cb-452c-b20c-78d0e3ee44ce/GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna.gz --refList GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/target_genomes_gtdb.txt --output GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:10:15,670] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:15,686] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:10:15,686] [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
GCF_009696165.1	s__Bulleidia intestinalis	97.6121	660	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	conclusive
GCA_900314905.1	s__Bulleidia sp900314905	89.1178	543	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900314345.1	s__Bulleidia sp900314345	77.4543	124	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900770275.1	s__Bulleidia sp900770275	77.4046	121	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433125.1	s__Bulleidia sp017433125	77.0916	60	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_015058875.1	s__Bulleidia sp015058875	77.0886	96	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.73	97.73	0.82	0.82	2	-
GCA_017469885.1	s__Bulleidia sp017469885	76.9229	95	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319505.1	s__Bulleidia sp900319505	76.8055	64	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.64	99.39	0.93	0.88	3	-
GCA_017420585.1	s__Bulleidia sp017420585	76.6486	57	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.75	98.73	0.84	0.83	3	-
GCA_905235315.1	s__Bulleidia sp905235315	76.6049	78	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775735.1	s__Bulleidia sp902775735	76.0824	52	780	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.20	97.93	0.87	0.80	4	-
--------------------------------------------------------------------------------
[2023-06-08 17:10:15,688] [INFO] GTDB search result was written to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/result_gtdb.tsv
[2023-06-08 17:10:15,689] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:10:15,699] [INFO] DFAST_QC result json was written to GCA_902795475.1_Rumen_uncultured_genome_RUG14074_genomic.fna/dqc_result.json
[2023-06-08 17:10:15,700] [INFO] DFAST_QC completed!
[2023-06-08 17:10:15,700] [INFO] Total running time: 0h0m57s