[2023-06-05 12:00:10,479] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:00:10,481] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:00:10,482] [INFO] DQC Reference Directory: /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference
[2023-06-05 12:00:12,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:00:12,723] [INFO] Task started: Prodigal
[2023-06-05 12:00:12,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgf66deed5-e41b-4568-889c-ee61dc4997e5/GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna.gz | prodigal -d GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/cds.fna -a GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:00:16,153] [INFO] Task succeeded: Prodigal
[2023-06-05 12:00:16,154] [INFO] Task started: HMMsearch
[2023-06-05 12:00:16,154] [INFO] Running command: hmmsearch --tblout GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/reference_markers.hmm GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:00:16,386] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:00:16,387] [INFO] Found 6/6 markers.
[2023-06-05 12:00:16,410] [INFO] Query marker FASTA was written to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/markers.fasta
[2023-06-05 12:00:16,411] [INFO] Task started: Blastn
[2023-06-05 12:00:16,411] [INFO] Running command: blastn -query GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/markers.fasta -db /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/reference_markers.fasta -out GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:00:17,725] [INFO] Task succeeded: Blastn
[2023-06-05 12:00:17,730] [INFO] Selected 20 target genomes.
[2023-06-05 12:00:17,730] [INFO] Target genome list was writen to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/target_genomes.txt
[2023-06-05 12:00:17,731] [INFO] Task started: fastANI
[2023-06-05 12:00:17,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66deed5-e41b-4568-889c-ee61dc4997e5/GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna.gz --refList GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/target_genomes.txt --output GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:00:28,348] [INFO] Task succeeded: fastANI
[2023-06-05 12:00:28,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:00:28,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:00:28,360] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:00:28,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:00:28,360] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.2411	52	457	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.0982	54	457	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.0696	65	457	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.9787	52	457	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8823	53	457	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:00:28,364] [INFO] DFAST Taxonomy check result was written to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/tc_result.tsv
[2023-06-05 12:00:28,364] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:00:28,365] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:00:28,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/checkm_data
[2023-06-05 12:00:28,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:00:28,387] [INFO] Task started: CheckM
[2023-06-05 12:00:28,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/checkm_input GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/checkm_result
[2023-06-05 12:00:46,243] [INFO] Task succeeded: CheckM
[2023-06-05 12:00:46,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:00:46,266] [INFO] ===== Completeness check finished =====
[2023-06-05 12:00:46,266] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:00:46,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/markers.fasta)
[2023-06-05 12:00:46,267] [INFO] Task started: Blastn
[2023-06-05 12:00:46,268] [INFO] Running command: blastn -query GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/markers.fasta -db /var/lib/cwl/stge7b5b6cb-ff3a-4183-b88e-fe2d593370e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:00:47,618] [INFO] Task succeeded: Blastn
[2023-06-05 12:00:47,622] [INFO] Selected 14 target genomes.
[2023-06-05 12:00:47,622] [INFO] Target genome list was writen to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:00:47,628] [INFO] Task started: fastANI
[2023-06-05 12:00:47,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgf66deed5-e41b-4568-889c-ee61dc4997e5/GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna.gz --refList GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/target_genomes_gtdb.txt --output GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:00:53,410] [INFO] Task succeeded: fastANI
[2023-06-05 12:00:53,421] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:00:53,422] [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_900315595.1	s__Faecousia sp900315595	97.8056	429	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.62	97.05	0.87	0.79	33	conclusive
GCA_017425545.1	s__Faecousia sp017425545	81.8625	206	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292255.1	s__Faecousia sp016292255	80.4568	210	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767915.1	s__Faecousia sp902767915	80.416	215	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.86	97.78	0.84	0.82	3	-
GCA_017519005.1	s__Faecousia sp017519005	80.1791	224	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.84	97.84	0.75	0.75	2	-
GCA_017541995.1	s__Faecousia sp017541995	79.9554	243	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540945.1	s__Faecousia sp017540945	79.8488	221	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.32	98.32	0.76	0.76	2	-
GCA_902795195.1	s__Faecousia sp902795195	79.6526	177	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395905.1	s__Avoscillospira_A sp904395905	76.779	69	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	76.7057	82	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067545.1	s__Faecousia sp015067545	76.6349	53	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436785.1	s__Faecousia sp017436785	76.1427	51	457	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:00:53,424] [INFO] GTDB search result was written to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/result_gtdb.tsv
[2023-06-05 12:00:53,425] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:00:53,429] [INFO] DFAST_QC result json was written to GCA_902769595.1_Rumen_uncultured_genome_RUG11484_genomic.fna/dqc_result.json
[2023-06-05 12:00:53,430] [INFO] DFAST_QC completed!
[2023-06-05 12:00:53,430] [INFO] Total running time: 0h0m43s