[2023-06-08 17:48:02,977] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:48:02,979] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:48:02,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference
[2023-06-08 17:48:04,262] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:48:04,264] [INFO] Task started: Prodigal
[2023-06-08 17:48:04,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg67eff3d6-d5bf-4b62-afc4-3ea96cdb340c/GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna.gz | prodigal -d GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/cds.fna -a GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:48:08,269] [INFO] Task succeeded: Prodigal
[2023-06-08 17:48:08,270] [INFO] Task started: HMMsearch
[2023-06-08 17:48:08,270] [INFO] Running command: hmmsearch --tblout GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/reference_markers.hmm GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:48:08,465] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:48:08,466] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg67eff3d6-d5bf-4b62-afc4-3ea96cdb340c/GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna.gz]
[2023-06-08 17:48:08,487] [INFO] Query marker FASTA was written to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/markers.fasta
[2023-06-08 17:48:08,488] [INFO] Task started: Blastn
[2023-06-08 17:48:08,488] [INFO] Running command: blastn -query GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/reference_markers.fasta -out GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:09,087] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:09,090] [INFO] Selected 26 target genomes.
[2023-06-08 17:48:09,091] [INFO] Target genome list was writen to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/target_genomes.txt
[2023-06-08 17:48:09,092] [INFO] Task started: fastANI
[2023-06-08 17:48:09,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg67eff3d6-d5bf-4b62-afc4-3ea96cdb340c/GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna.gz --refList GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/target_genomes.txt --output GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:48:23,712] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:23,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:48:23,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:48:23,717] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 17:48:23,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 17:48:23,717] [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
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	98.553	397	456	95	conclusive
--------------------------------------------------------------------------------
[2023-06-08 17:48:23,721] [INFO] DFAST Taxonomy check result was written to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/tc_result.tsv
[2023-06-08 17:48:23,722] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:48:23,722] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:48:23,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/checkm_data
[2023-06-08 17:48:23,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:48:23,742] [INFO] Task started: CheckM
[2023-06-08 17:48:23,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/checkm_input GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/checkm_result
[2023-06-08 17:48:43,608] [INFO] Task succeeded: CheckM
[2023-06-08 17:48:43,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:48:43,625] [INFO] ===== Completeness check finished =====
[2023-06-08 17:48:43,625] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:48:43,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/markers.fasta)
[2023-06-08 17:48:43,625] [INFO] Task started: Blastn
[2023-06-08 17:48:43,626] [INFO] Running command: blastn -query GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bbb082f-ceef-43eb-be2e-51c9088ec6da/dqc_reference/reference_markers_gtdb.fasta -out GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:44,439] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:44,458] [INFO] Selected 21 target genomes.
[2023-06-08 17:48:44,458] [INFO] Target genome list was writen to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:48:44,467] [INFO] Task started: fastANI
[2023-06-08 17:48:44,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg67eff3d6-d5bf-4b62-afc4-3ea96cdb340c/GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna.gz --refList GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/target_genomes_gtdb.txt --output GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:52,147] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:52,156] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:48:52,156] [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_900343155.1	s__Bulleidia massiliensis	98.553	397	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.00	97.48	0.85	0.81	18	conclusive
GCA_900319505.1	s__Bulleidia sp900319505	78.3691	113	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.64	99.39	0.93	0.88	3	-
GCA_900315065.1	s__Bulleidia sp900315065	78.2343	97	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.99	99.99	0.97	0.97	2	-
GCA_000701725.1	s__Bulleidia sp000701725	77.4701	63	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.69	96.78	0.88	0.87	6	-
GCA_905201565.1	s__Bulleidia sp905201565	77.2551	81	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696165.1	s__Bulleidia intestinalis	76.9546	85	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	-
GCA_017539385.1	s__Bulleidia sp017539385	76.8481	58	456	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	76.6298	57	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_017543005.1	s__Bulleidia sp017543005	76.4119	61	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.24	98.24	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:52,159] [INFO] GTDB search result was written to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:52,159] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:52,162] [INFO] DFAST_QC result json was written to GCA_902803905.1_Rumen_uncultured_genome_RUG14917_genomic.fna/dqc_result.json
[2023-06-08 17:48:52,162] [INFO] DFAST_QC completed!
[2023-06-08 17:48:52,162] [INFO] Total running time: 0h0m49s