[2023-06-07 21:13:30,488] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:30,491] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:30,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference
[2023-06-07 21:13:33,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:33,294] [INFO] Task started: Prodigal
[2023-06-07 21:13:33,295] [INFO] Running command: gunzip -c /var/lib/cwl/stgb91a1fa6-9954-4850-a35a-71d073698d46/GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna.gz | prodigal -d GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/cds.fna -a GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:45,949] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:45,949] [INFO] Task started: HMMsearch
[2023-06-07 21:13:45,950] [INFO] Running command: hmmsearch --tblout GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/reference_markers.hmm GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:46,181] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:46,183] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb91a1fa6-9954-4850-a35a-71d073698d46/GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna.gz]
[2023-06-07 21:13:46,210] [INFO] Query marker FASTA was written to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/markers.fasta
[2023-06-07 21:13:46,211] [INFO] Task started: Blastn
[2023-06-07 21:13:46,211] [INFO] Running command: blastn -query GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/reference_markers.fasta -out GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:46,841] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:46,844] [INFO] Selected 24 target genomes.
[2023-06-07 21:13:46,845] [INFO] Target genome list was writen to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/target_genomes.txt
[2023-06-07 21:13:46,849] [INFO] Task started: fastANI
[2023-06-07 21:13:46,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91a1fa6-9954-4850-a35a-71d073698d46/GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna.gz --refList GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/target_genomes.txt --output GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:14:01,632] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:01,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:14:01,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:14:01,643] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:14:01,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:14:01,643] [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
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.3244	51	752	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	77.3146	54	752	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	77.2677	55	752	95	below_threshold
Bacteroides cutis	strain=Marseille-P4118	GCA_900241005.1	2024197	2024197	type	True	77.0392	55	752	95	below_threshold
Bacteroides heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	76.8313	54	752	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	76.7851	53	752	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	76.7421	54	752	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	76.5969	60	752	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	76.4907	57	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:14:01,645] [INFO] DFAST Taxonomy check result was written to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/tc_result.tsv
[2023-06-07 21:14:01,646] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:14:01,646] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:14:01,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/checkm_data
[2023-06-07 21:14:01,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:14:01,677] [INFO] Task started: CheckM
[2023-06-07 21:14:01,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/checkm_input GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/checkm_result
[2023-06-07 21:14:42,166] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:42,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:42,195] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:42,196] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:42,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/markers.fasta)
[2023-06-07 21:14:42,197] [INFO] Task started: Blastn
[2023-06-07 21:14:42,197] [INFO] Running command: blastn -query GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c13528f-6d3d-4361-9782-e26d8d4395ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:42,942] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:42,947] [INFO] Selected 9 target genomes.
[2023-06-07 21:14:42,948] [INFO] Target genome list was writen to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:42,954] [INFO] Task started: fastANI
[2023-06-07 21:14:42,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgb91a1fa6-9954-4850-a35a-71d073698d46/GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna.gz --refList GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/target_genomes_gtdb.txt --output GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:47,613] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:47,623] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:14:47,624] [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_902775375.1	s__UBA2918 sp002349865	98.213	692	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	98.32	97.59	0.93	0.86	10	conclusive
GCA_902779085.1	s__UBA2918 sp902779085	85.5822	601	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442855.1	s__UBA2918 sp017442855	81.8066	419	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284115.1	s__UBA2918 sp016284115	81.5117	346	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651505.1	s__UBA2918 sp017651505	81.1637	291	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534535.1	s__UBA2918 sp017534535	80.6395	365	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313715.1	s__UBA2918 sp900313715	80.5449	324	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902783615.1	s__UBA2918 sp902783615	78.8349	252	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA2918	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:47,626] [INFO] GTDB search result was written to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:47,626] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:47,632] [INFO] DFAST_QC result json was written to GCA_902765355.1_Rumen_uncultured_genome_RUG11053_genomic.fna/dqc_result.json
[2023-06-07 21:14:47,632] [INFO] DFAST_QC completed!
[2023-06-07 21:14:47,632] [INFO] Total running time: 0h1m17s