[2023-06-08 08:10:26,205] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:10:26,207] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:10:26,208] [INFO] DQC Reference Directory: /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference
[2023-06-08 08:10:27,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:10:27,820] [INFO] Task started: Prodigal
[2023-06-08 08:10:27,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg32e7def4-c9d9-488d-b23f-d7312a6c40a8/GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna.gz | prodigal -d GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/cds.fna -a GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:10:35,226] [INFO] Task succeeded: Prodigal
[2023-06-08 08:10:35,226] [INFO] Task started: HMMsearch
[2023-06-08 08:10:35,226] [INFO] Running command: hmmsearch --tblout GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/reference_markers.hmm GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:10:35,504] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:10:35,505] [INFO] Found 6/6 markers.
[2023-06-08 08:10:35,533] [INFO] Query marker FASTA was written to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/markers.fasta
[2023-06-08 08:10:35,533] [INFO] Task started: Blastn
[2023-06-08 08:10:35,534] [INFO] Running command: blastn -query GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/markers.fasta -db /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/reference_markers.fasta -out GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:10:36,308] [INFO] Task succeeded: Blastn
[2023-06-08 08:10:36,313] [INFO] Selected 13 target genomes.
[2023-06-08 08:10:36,313] [INFO] Target genome list was writen to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/target_genomes.txt
[2023-06-08 08:10:36,315] [INFO] Task started: fastANI
[2023-06-08 08:10:36,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e7def4-c9d9-488d-b23f-d7312a6c40a8/GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna.gz --refList GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/target_genomes.txt --output GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:10:44,374] [INFO] Task succeeded: fastANI
[2023-06-08 08:10:44,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:10:44,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:10:44,384] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:10:44,384] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:10:44,384] [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
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	79.6744	338	808	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	79.5607	343	808	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	77.3133	170	808	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.0134	113	808	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	76.9342	94	808	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	76.605	152	808	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	76.6016	100	808	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	76.5555	156	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:10:44,386] [INFO] DFAST Taxonomy check result was written to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/tc_result.tsv
[2023-06-08 08:10:44,387] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:10:44,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:10:44,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/checkm_data
[2023-06-08 08:10:44,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:10:44,422] [INFO] Task started: CheckM
[2023-06-08 08:10:44,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/checkm_input GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/checkm_result
[2023-06-08 08:11:11,617] [INFO] Task succeeded: CheckM
[2023-06-08 08:11:11,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:11:11,642] [INFO] ===== Completeness check finished =====
[2023-06-08 08:11:11,643] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:11:11,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/markers.fasta)
[2023-06-08 08:11:11,643] [INFO] Task started: Blastn
[2023-06-08 08:11:11,644] [INFO] Running command: blastn -query GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/markers.fasta -db /var/lib/cwl/stgc816347f-a3ea-49a2-9942-0f645b384a72/dqc_reference/reference_markers_gtdb.fasta -out GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:11:12,635] [INFO] Task succeeded: Blastn
[2023-06-08 08:11:12,639] [INFO] Selected 12 target genomes.
[2023-06-08 08:11:12,639] [INFO] Target genome list was writen to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:11:12,641] [INFO] Task started: fastANI
[2023-06-08 08:11:12,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e7def4-c9d9-488d-b23f-d7312a6c40a8/GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna.gz --refList GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/target_genomes_gtdb.txt --output GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:11:19,264] [INFO] Task succeeded: fastANI
[2023-06-08 08:11:19,277] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:11:19,278] [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_002350105.1	s__UBA2897 sp002350105	99.8507	742	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA2897	95.0	98.95	98.43	0.90	0.80	8	conclusive
GCA_900316275.1	s__UBA2897 sp900316275	81.9988	449	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA2897	95.0	99.98	99.98	0.97	0.97	2	-
GCA_900315155.1	s__UBA2897 sp900315155	81.3788	461	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA2897	95.0	99.70	99.40	0.95	0.90	3	-
GCF_000702905.1	s__Mitsuokella jalaludinii	79.6683	338	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
GCF_000155955.1	s__Mitsuokella multacida	79.5649	344	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	-
GCF_000381005.1	s__Selenomonas_C bovis	79.1589	306	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.36	95.92	0.90	0.82	11	-
GCA_902364065.1	s__Mitsuokella sp003458855	79.1434	317	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.62	95.79	0.87	0.62	6	-
GCA_900315575.1	s__Selenomonas_C sp900315575	78.7215	319	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.63	0.83	0.78	4	-
GCA_902763085.1	s__Selenomonas_C sp002351185	78.5275	282	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.44	97.41	0.83	0.79	3	-
GCA_900314825.1	s__Selenomonas_C sp900314825	78.4602	307	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900113715.1	s__Selenomonas_A ruminantium_F	78.1576	256	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	97.92	97.43	0.89	0.84	3	-
GCF_000284095.1	s__Selenomonas_A lactilytica	77.3122	167	808	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:11:19,280] [INFO] GTDB search result was written to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/result_gtdb.tsv
[2023-06-08 08:11:19,280] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:11:19,283] [INFO] DFAST_QC result json was written to GCA_902802655.1_Rumen_uncultured_genome_RUG14795_genomic.fna/dqc_result.json
[2023-06-08 08:11:19,284] [INFO] DFAST_QC completed!
[2023-06-08 08:11:19,284] [INFO] Total running time: 0h0m53s