[2023-06-08 14:09:59,789] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:09:59,796] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:09:59,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference
[2023-06-08 14:10:02,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:10:02,087] [INFO] Task started: Prodigal
[2023-06-08 14:10:02,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg00498bac-3d9b-443b-8dcb-10daba68aa40/GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna.gz | prodigal -d GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/cds.fna -a GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:10:13,085] [INFO] Task succeeded: Prodigal
[2023-06-08 14:10:13,086] [INFO] Task started: HMMsearch
[2023-06-08 14:10:13,086] [INFO] Running command: hmmsearch --tblout GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/reference_markers.hmm GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:10:13,327] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:10:13,329] [INFO] Found 6/6 markers.
[2023-06-08 14:10:13,367] [INFO] Query marker FASTA was written to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/markers.fasta
[2023-06-08 14:10:13,368] [INFO] Task started: Blastn
[2023-06-08 14:10:13,368] [INFO] Running command: blastn -query GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/reference_markers.fasta -out GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:10:13,987] [INFO] Task succeeded: Blastn
[2023-06-08 14:10:13,991] [INFO] Selected 19 target genomes.
[2023-06-08 14:10:13,991] [INFO] Target genome list was writen to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/target_genomes.txt
[2023-06-08 14:10:13,993] [INFO] Task started: fastANI
[2023-06-08 14:10:13,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg00498bac-3d9b-443b-8dcb-10daba68aa40/GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna.gz --refList GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/target_genomes.txt --output GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:10:20,471] [INFO] Task succeeded: fastANI
[2023-06-08 14:10:20,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:10:20,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:10:20,484] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:10:20,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:10:20,484] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	77.2634	121	1101	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	77.0928	76	1101	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	77.0575	73	1101	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	77.0183	78	1101	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	76.9507	91	1101	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	76.9224	87	1101	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	76.8322	96	1101	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	76.5021	62	1101	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	76.1496	54	1101	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:10:20,486] [INFO] DFAST Taxonomy check result was written to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/tc_result.tsv
[2023-06-08 14:10:20,487] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:10:20,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:10:20,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/checkm_data
[2023-06-08 14:10:20,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:10:20,526] [INFO] Task started: CheckM
[2023-06-08 14:10:20,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/checkm_input GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/checkm_result
[2023-06-08 14:10:56,309] [INFO] Task succeeded: CheckM
[2023-06-08 14:10:56,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 14:10:56,334] [INFO] ===== Completeness check finished =====
[2023-06-08 14:10:56,335] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:10:56,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/markers.fasta)
[2023-06-08 14:10:56,335] [INFO] Task started: Blastn
[2023-06-08 14:10:56,335] [INFO] Running command: blastn -query GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcfef22f-6f10-40dc-b2fd-1a594ee9736d/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:10:57,230] [INFO] Task succeeded: Blastn
[2023-06-08 14:10:57,235] [INFO] Selected 12 target genomes.
[2023-06-08 14:10:57,235] [INFO] Target genome list was writen to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:10:57,243] [INFO] Task started: fastANI
[2023-06-08 14:10:57,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg00498bac-3d9b-443b-8dcb-10daba68aa40/GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna.gz --refList GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/target_genomes_gtdb.txt --output GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:11:05,110] [INFO] Task succeeded: fastANI
[2023-06-08 14:11:05,126] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:11:05,126] [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_902766445.1	s__RUG440 sp902766445	100.0	1088	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	98.05	98.05	0.80	0.80	2	conclusive
GCA_900318935.1	s__RUG440 sp900318935	93.7833	710	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	99.08	99.08	0.86	0.86	2	-
GCA_902798915.1	s__RUG440 sp902798915	80.0862	382	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017533825.1	s__RUG440 sp017533825	80.0151	368	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	97.87	97.87	0.75	0.75	2	-
GCA_902786015.1	s__RUG440 sp902786015	78.5008	235	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017510785.1	s__RUG440 sp017510785	78.2805	237	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780305.1	s__RUG440 sp902780305	78.2232	210	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777325.1	s__UBA1367 sp902777325	78.0036	190	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235165.1	s__UBA1367 sp905235165	77.5063	90	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803315.1	s__RUG440 sp902803315	77.2398	151	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117265.1	s__Thermophilibacter pullicola	77.0142	80	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	76.1844	53	1101	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-08 14:11:05,128] [INFO] GTDB search result was written to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/result_gtdb.tsv
[2023-06-08 14:11:05,129] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:11:05,133] [INFO] DFAST_QC result json was written to GCA_902766445.1_Rumen_uncultured_genome_RUG11163_genomic.fna/dqc_result.json
[2023-06-08 14:11:05,134] [INFO] DFAST_QC completed!
[2023-06-08 14:11:05,134] [INFO] Total running time: 0h1m5s