[2023-06-08 14:46:48,318] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:48,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:48,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference
[2023-06-08 14:46:49,960] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:49,961] [INFO] Task started: Prodigal
[2023-06-08 14:46:49,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf966f46-2b5c-4135-9997-0f21c9534092/GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna.gz | prodigal -d GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/cds.fna -a GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:54,651] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:54,651] [INFO] Task started: HMMsearch
[2023-06-08 14:46:54,651] [INFO] Running command: hmmsearch --tblout GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/reference_markers.hmm GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:54,870] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:54,872] [INFO] Found 6/6 markers.
[2023-06-08 14:46:54,891] [INFO] Query marker FASTA was written to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/markers.fasta
[2023-06-08 14:46:54,891] [INFO] Task started: Blastn
[2023-06-08 14:46:54,891] [INFO] Running command: blastn -query GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/reference_markers.fasta -out GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:55,676] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:55,680] [INFO] Selected 14 target genomes.
[2023-06-08 14:46:55,681] [INFO] Target genome list was writen to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/target_genomes.txt
[2023-06-08 14:46:55,683] [INFO] Task started: fastANI
[2023-06-08 14:46:55,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf966f46-2b5c-4135-9997-0f21c9534092/GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna.gz --refList GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/target_genomes.txt --output GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:47:03,157] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:03,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:47:03,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:47:03,173] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 14:47:03,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 14:47:03,174] [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	97.6322	500	533	95	conclusive
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	81.2623	249	533	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	81.0946	258	533	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	80.9565	260	533	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.7711	269	533	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.4958	257	533	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	80.3786	209	533	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	80.0588	227	533	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.9706	227	533	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	75.2199	75	533	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.7765	86	533	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:47:03,176] [INFO] DFAST Taxonomy check result was written to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/tc_result.tsv
[2023-06-08 14:47:03,176] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:47:03,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:47:03,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/checkm_data
[2023-06-08 14:47:03,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:47:03,205] [INFO] Task started: CheckM
[2023-06-08 14:47:03,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/checkm_input GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/checkm_result
[2023-06-08 14:47:23,767] [INFO] Task succeeded: CheckM
[2023-06-08 14:47:23,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.18%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:47:23,791] [INFO] ===== Completeness check finished =====
[2023-06-08 14:47:23,791] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:47:23,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/markers.fasta)
[2023-06-08 14:47:23,792] [INFO] Task started: Blastn
[2023-06-08 14:47:23,792] [INFO] Running command: blastn -query GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4e5230c-ddcf-4fbb-96c3-bbd7f9d24d97/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:25,188] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:25,202] [INFO] Selected 21 target genomes.
[2023-06-08 14:47:25,202] [INFO] Target genome list was writen to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:47:25,218] [INFO] Task started: fastANI
[2023-06-08 14:47:25,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf966f46-2b5c-4135-9997-0f21c9534092/GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna.gz --refList GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/target_genomes_gtdb.txt --output GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:33,793] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:33,811] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:47:33,811] [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_902780325.1	s__Parafannyhessea sp902787335	97.9448	391	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	conclusive
GCA_017941585.1	s__Parafannyhessea sp017941585	82.9599	296	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111255.1	s__Parafannyhessea umbonata_A	82.0986	298	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	99.32	99.30	0.95	0.94	4	-
GCA_003862195.1	s__Parafannyhessea sp003862195	81.9725	279	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_012844235.1	s__Parafannyhessea sp900538935	81.4173	284	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCF_900120385.1	s__Olsenella_I phocaeensis	81.2381	251	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCA_900314575.1	s__UBA7741 sp900314575	81.1449	259	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_900105025.1	s__Parafannyhessea umbonata	81.0841	275	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCF_002159735.1	s__Thermophilibacter sp002159735	81.0309	260	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143845.1	s__Olsenella uli	80.9565	260	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.861	260	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	80.7714	269	533	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	80.6848	217	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777325.1	s__UBA1367 sp902777325	80.6795	250	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772435.1	s__UBA1367 sp902772435	80.5906	223	533	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	80.108	249	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCF_001457795.1	s__Olsenella_F massiliensis	79.9942	226	533	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	98.66	97.33	0.97	0.93	3	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:33,813] [INFO] GTDB search result was written to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:33,814] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:33,818] [INFO] DFAST_QC result json was written to GCA_902763695.1_Rumen_uncultured_genome_RUG10887_genomic.fna/dqc_result.json
[2023-06-08 14:47:33,818] [INFO] DFAST_QC completed!
[2023-06-08 14:47:33,818] [INFO] Total running time: 0h0m46s