[2023-06-08 13:32:12,366] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:32:12,368] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:32:12,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference
[2023-06-08 13:32:14,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:32:14,083] [INFO] Task started: Prodigal
[2023-06-08 13:32:14,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf661884-8e4d-49f9-99b6-c9831de9a641/GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna.gz | prodigal -d GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/cds.fna -a GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:32:22,152] [INFO] Task succeeded: Prodigal
[2023-06-08 13:32:22,152] [INFO] Task started: HMMsearch
[2023-06-08 13:32:22,153] [INFO] Running command: hmmsearch --tblout GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/reference_markers.hmm GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:32:22,392] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:32:22,393] [INFO] Found 6/6 markers.
[2023-06-08 13:32:22,427] [INFO] Query marker FASTA was written to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/markers.fasta
[2023-06-08 13:32:22,427] [INFO] Task started: Blastn
[2023-06-08 13:32:22,427] [INFO] Running command: blastn -query GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/markers.fasta -db /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/reference_markers.fasta -out GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:32:23,079] [INFO] Task succeeded: Blastn
[2023-06-08 13:32:23,086] [INFO] Selected 14 target genomes.
[2023-06-08 13:32:23,087] [INFO] Target genome list was writen to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/target_genomes.txt
[2023-06-08 13:32:23,090] [INFO] Task started: fastANI
[2023-06-08 13:32:23,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf661884-8e4d-49f9-99b6-c9831de9a641/GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna.gz --refList GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/target_genomes.txt --output GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:32:31,192] [INFO] Task succeeded: fastANI
[2023-06-08 13:32:31,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:32:31,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:32:31,202] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:32:31,202] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:32:31,202] [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 phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.4541	244	896	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.4094	208	896	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.3242	251	896	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.3194	243	896	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.0658	247	896	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.0346	224	896	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.0164	222	896	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	78.9463	215	896	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.7232	214	896	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	78.2476	158	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:32:31,204] [INFO] DFAST Taxonomy check result was written to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/tc_result.tsv
[2023-06-08 13:32:31,205] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:32:31,205] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:32:31,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/checkm_data
[2023-06-08 13:32:31,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:32:31,235] [INFO] Task started: CheckM
[2023-06-08 13:32:31,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/checkm_input GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/checkm_result
[2023-06-08 13:32:57,803] [INFO] Task succeeded: CheckM
[2023-06-08 13:32:57,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:32:57,834] [INFO] ===== Completeness check finished =====
[2023-06-08 13:32:57,834] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:32:57,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/markers.fasta)
[2023-06-08 13:32:57,835] [INFO] Task started: Blastn
[2023-06-08 13:32:57,835] [INFO] Running command: blastn -query GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/markers.fasta -db /var/lib/cwl/stg6978f84f-efd5-429f-99e0-2e823c65eaf1/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:32:58,880] [INFO] Task succeeded: Blastn
[2023-06-08 13:32:58,884] [INFO] Selected 21 target genomes.
[2023-06-08 13:32:58,884] [INFO] Target genome list was writen to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:32:58,928] [INFO] Task started: fastANI
[2023-06-08 13:32:58,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf661884-8e4d-49f9-99b6-c9831de9a641/GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna.gz --refList GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/target_genomes_gtdb.txt --output GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:33:08,753] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:08,766] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:33:08,766] [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_900314495.1	s__UBA7741 sp900314495	100.0	891	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	98.85	98.57	0.91	0.87	9	conclusive
GCA_902791035.1	s__CADAUA01 sp900315375	80.7083	355	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CADAUA01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_900314575.1	s__UBA7741 sp900314575	80.334	301	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_003416765.1	s__Paratractidigestivibacter faecalis	79.9897	267	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.79	95.48	0.89	0.83	10	-
GCA_900314685.1	s__Olegusella sp900314685	79.7344	285	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olegusella	95.0	99.04	98.52	0.90	0.85	10	-
GCA_905215465.1	s__Paratractidigestivibacter sp905215465	79.6456	248	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214865.1	s__Olsenella_H sp905214865	79.6018	285	896	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_900315165.1	s__Olegusella sp900315165	79.4574	260	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olegusella	95.0	98.60	95.39	0.90	0.84	7	-
GCA_900316105.1	s__Olsenella_F sp900316105	79.4524	257	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	99.68	99.68	0.95	0.93	3	-
GCF_016899935.1	s__Thermophilibacter uli_B	79.4311	258	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	79.2568	260	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982725.1	s__Thermophilibacter sp014982725	79.2219	246	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	79.203	277	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.1559	198	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305805.1	s__Thermophilibacter excrementavium	79.1062	214	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.86	97.86	0.86	0.86	2	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	79.0472	248	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778135.1	s__UBA1367 sp902778135	78.9596	241	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
GCF_015277515.1	s__Thermophilibacter sp002407785	78.7232	214	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	98.98	98.98	0.86	0.86	2	-
GCA_902780305.1	s__RUG440 sp902780305	78.4399	180	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017941585.1	s__Parafannyhessea sp017941585	78.4355	173	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460265.1	s__UBA1367 sp017460265	78.2161	155	896	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:33:08,768] [INFO] GTDB search result was written to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/result_gtdb.tsv
[2023-06-08 13:33:08,768] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:33:08,771] [INFO] DFAST_QC result json was written to GCA_902757255.1_Rumen_uncultured_genome_RUG10246_genomic.fna/dqc_result.json
[2023-06-08 13:33:08,771] [INFO] DFAST_QC completed!
[2023-06-08 13:33:08,772] [INFO] Total running time: 0h0m56s