[2023-06-05 13:15:32,997] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:15:32,999] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:15:32,999] [INFO] DQC Reference Directory: /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference
[2023-06-05 13:15:34,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:15:34,552] [INFO] Task started: Prodigal
[2023-06-05 13:15:34,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dbd7290-bfe9-4240-a479-b445bf404cf5/GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna.gz | prodigal -d GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/cds.fna -a GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:15:40,561] [INFO] Task succeeded: Prodigal
[2023-06-05 13:15:40,562] [INFO] Task started: HMMsearch
[2023-06-05 13:15:40,562] [INFO] Running command: hmmsearch --tblout GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/reference_markers.hmm GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:15:40,716] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:15:40,717] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2dbd7290-bfe9-4240-a479-b445bf404cf5/GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna.gz]
[2023-06-05 13:15:40,737] [INFO] Query marker FASTA was written to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/markers.fasta
[2023-06-05 13:15:40,737] [INFO] Task started: Blastn
[2023-06-05 13:15:40,738] [INFO] Running command: blastn -query GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/markers.fasta -db /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/reference_markers.fasta -out GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:15:41,370] [INFO] Task succeeded: Blastn
[2023-06-05 13:15:41,373] [INFO] Selected 12 target genomes.
[2023-06-05 13:15:41,373] [INFO] Target genome list was writen to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/target_genomes.txt
[2023-06-05 13:15:41,376] [INFO] Task started: fastANI
[2023-06-05 13:15:41,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dbd7290-bfe9-4240-a479-b445bf404cf5/GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna.gz --refList GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/target_genomes.txt --output GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:15:47,901] [INFO] Task succeeded: fastANI
[2023-06-05 13:15:47,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:15:47,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:15:47,910] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:15:47,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:15:47,910] [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
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.1643	272	683	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.0548	243	683	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.0534	292	683	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.8817	265	683	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.7147	274	683	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.495	242	683	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.4672	244	683	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.4446	209	683	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.399	213	683	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	77.9152	82	683	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:15:47,912] [INFO] DFAST Taxonomy check result was written to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/tc_result.tsv
[2023-06-05 13:15:47,913] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:15:47,913] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:15:47,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/checkm_data
[2023-06-05 13:15:47,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:15:47,942] [INFO] Task started: CheckM
[2023-06-05 13:15:47,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/checkm_input GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/checkm_result
[2023-06-05 13:16:09,421] [INFO] Task succeeded: CheckM
[2023-06-05 13:16:09,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:16:09,439] [INFO] ===== Completeness check finished =====
[2023-06-05 13:16:09,439] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:16:09,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/markers.fasta)
[2023-06-05 13:16:09,440] [INFO] Task started: Blastn
[2023-06-05 13:16:09,440] [INFO] Running command: blastn -query GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/markers.fasta -db /var/lib/cwl/stga9af1a04-4f88-4fff-9f04-8571a0cf3766/dqc_reference/reference_markers_gtdb.fasta -out GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:16:10,579] [INFO] Task succeeded: Blastn
[2023-06-05 13:16:10,582] [INFO] Selected 20 target genomes.
[2023-06-05 13:16:10,582] [INFO] Target genome list was writen to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:16:10,597] [INFO] Task started: fastANI
[2023-06-05 13:16:10,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dbd7290-bfe9-4240-a479-b445bf404cf5/GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna.gz --refList GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/target_genomes_gtdb.txt --output GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:16:19,479] [INFO] Task succeeded: fastANI
[2023-06-05 13:16:19,489] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:16:19,489] [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_900548775.1	s__Tractidigestivibacter sp900548775	98.6161	539	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.69	98.21	0.83	0.74	10	conclusive
GCF_900119625.1	s__Tractidigestivibacter sp900119625	90.1932	555	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCF_900111695.1	s__Tractidigestivibacter sp900111695	89.953	559	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	89.7578	507	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCA_900768455.1	s__Tractidigestivibacter sp900768455	88.4886	462	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	97.35	97.35	0.93	0.93	2	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	88.257	549	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	88.1038	538	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_905214175.1	s__Tractidigestivibacter sp905214175	87.8431	355	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	87.5646	374	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	86.3559	487	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844235.1	s__Parafannyhessea sp900538935	80.5134	279	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCA_003862195.1	s__Parafannyhessea sp003862195	80.4471	296	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_900105025.1	s__Parafannyhessea umbonata	80.4412	285	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.3339	279	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.1403	198	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
--------------------------------------------------------------------------------
[2023-06-05 13:16:19,490] [INFO] GTDB search result was written to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/result_gtdb.tsv
[2023-06-05 13:16:19,491] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:16:19,494] [INFO] DFAST_QC result json was written to GCA_902792205.1_Rumen_uncultured_genome_RUG13750_genomic.fna/dqc_result.json
[2023-06-05 13:16:19,494] [INFO] DFAST_QC completed!
[2023-06-05 13:16:19,494] [INFO] Total running time: 0h0m46s