[2023-06-08 17:09:13,520] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:13,522] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:13,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference
[2023-06-08 17:09:14,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:14,802] [INFO] Task started: Prodigal
[2023-06-08 17:09:14,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg990664ef-194a-4bf6-81e9-14851bce2c71/GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna.gz | prodigal -d GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/cds.fna -a GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:21,640] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:21,640] [INFO] Task started: HMMsearch
[2023-06-08 17:09:21,640] [INFO] Running command: hmmsearch --tblout GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/reference_markers.hmm GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:21,885] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:21,886] [INFO] Found 6/6 markers.
[2023-06-08 17:09:21,920] [INFO] Query marker FASTA was written to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/markers.fasta
[2023-06-08 17:09:21,921] [INFO] Task started: Blastn
[2023-06-08 17:09:21,921] [INFO] Running command: blastn -query GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/reference_markers.fasta -out GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:22,591] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:22,595] [INFO] Selected 13 target genomes.
[2023-06-08 17:09:22,595] [INFO] Target genome list was writen to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/target_genomes.txt
[2023-06-08 17:09:22,596] [INFO] Task started: fastANI
[2023-06-08 17:09:22,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg990664ef-194a-4bf6-81e9-14851bce2c71/GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna.gz --refList GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/target_genomes.txt --output GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:27,085] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:27,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:27,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:27,097] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:27,097] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:09:27,098] [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	80.5881	240	677	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.7886	207	677	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.665	230	677	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.6167	233	677	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.5596	162	677	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.2014	187	677	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.0866	197	677	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	78.9304	178	677	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.9218	172	677	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.9105	165	677	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.9045	199	677	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	77.2877	70	677	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	77.1762	72	677	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:27,100] [INFO] DFAST Taxonomy check result was written to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/tc_result.tsv
[2023-06-08 17:09:27,100] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:27,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:27,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/checkm_data
[2023-06-08 17:09:27,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:27,141] [INFO] Task started: CheckM
[2023-06-08 17:09:27,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/checkm_input GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/checkm_result
[2023-06-08 17:09:53,222] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:53,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:53,247] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:53,247] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:53,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/markers.fasta)
[2023-06-08 17:09:53,248] [INFO] Task started: Blastn
[2023-06-08 17:09:53,248] [INFO] Running command: blastn -query GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d96b171-d442-44bf-95eb-4a7abfd261e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:54,397] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:54,401] [INFO] Selected 18 target genomes.
[2023-06-08 17:09:54,401] [INFO] Target genome list was writen to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:54,407] [INFO] Task started: fastANI
[2023-06-08 17:09:54,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg990664ef-194a-4bf6-81e9-14851bce2c71/GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna.gz --refList GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/target_genomes_gtdb.txt --output GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:10:02,789] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:02,805] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:10:02,805] [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_902772435.1	s__UBA1367 sp902772435	100.0	668	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902777325.1	s__UBA1367 sp902777325	82.3303	348	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779675.1	s__UBA1367 sp902779675	81.8473	342	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCA_900314645.1	s__UBA1367 sp900314645	81.6097	336	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.42	97.54	0.93	0.89	4	-
GCA_902788705.1	s__UBA1367 sp902788705	81.5196	330	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.66	97.66	0.87	0.87	2	-
GCA_902778135.1	s__UBA1367 sp902778135	81.4163	333	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
GCA_002449555.1	s__UBA1367 sp002449555	81.1902	272	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801175.1	s__UBA1367 sp902801175	81.1076	307	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	95.50	95.48	0.84	0.83	3	-
GCA_017460265.1	s__UBA1367 sp017460265	81.0863	254	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.6686	207	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_014982725.1	s__Thermophilibacter sp014982725	80.2105	218	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797175.1	s__UBA1367 sp902797175	80.2101	286	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	80.0851	226	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.889	187	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791035.1	s__CADAUA01 sp900315375	79.4994	243	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CADAUA01	95.0	99.88	99.88	0.96	0.96	2	-
GCF_900105025.1	s__Parafannyhessea umbonata	79.0238	203	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCA_019117005.1	s__Collinsella stercoripullorum	78.6783	146	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCA_017652285.1	s__RUG440 sp017652285	78.612	183	677	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:10:02,812] [INFO] GTDB search result was written to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/result_gtdb.tsv
[2023-06-08 17:10:02,813] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:10:02,818] [INFO] DFAST_QC result json was written to GCA_902772435.1_Rumen_uncultured_genome_RUG11770_genomic.fna/dqc_result.json
[2023-06-08 17:10:02,818] [INFO] DFAST_QC completed!
[2023-06-08 17:10:02,818] [INFO] Total running time: 0h0m49s