[2024-01-24 13:32:41,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference
[2024-01-24 13:32:42,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,388] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg223ce5e3-e1aa-44a0-8965-49abc10ac5ce/GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna.gz | prodigal -d GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/cds.fna -a GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:45,296] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:45,296] [INFO] Task started: HMMsearch
[2024-01-24 13:32:45,296] [INFO] Running command: hmmsearch --tblout GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/reference_markers.hmm GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:45,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:45,519] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg223ce5e3-e1aa-44a0-8965-49abc10ac5ce/GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna.gz]
[2024-01-24 13:32:45,538] [INFO] Query marker FASTA was written to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/markers.fasta
[2024-01-24 13:32:45,538] [INFO] Task started: Blastn
[2024-01-24 13:32:45,538] [INFO] Running command: blastn -query GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/reference_markers.fasta -out GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:46,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:46,068] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:46,069] [INFO] Target genome list was writen to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,440] [INFO] Task started: fastANI
[2024-01-24 13:32:46,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg223ce5e3-e1aa-44a0-8965-49abc10ac5ce/GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna.gz --refList GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/target_genomes.txt --output GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:55,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:55,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:55,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:55,246] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:55,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:55,246] [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
Eggerthia catenaformis	strain=OT 569	GCA_000340375.1	31973	31973	type	True	99.9999	636	644	95	conclusive
Eggerthia catenaformis	strain=DSM 20559	GCA_000422605.1	31973	31973	type	True	98.7766	554	644	95	conclusive
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	78.1684	111	644	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.9119	85	644	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.9026	57	644	95	below_threshold
Sharpea porci	strain=CA-Schmier-601-WT-3	GCA_009695655.1	2652286	2652286	type	True	77.6609	112	644	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	77.0068	106	644	95	below_threshold
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	76.5231	78	644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:55,247] [INFO] DFAST Taxonomy check result was written to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:55,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:55,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:55,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/checkm_data
[2024-01-24 13:32:55,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:55,270] [INFO] Task started: CheckM
[2024-01-24 13:32:55,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/checkm_input GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/checkm_result
[2024-01-24 13:33:10,898] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:10,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,933] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:10,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:10,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/markers.fasta)
[2024-01-24 13:33:10,934] [INFO] Task started: Blastn
[2024-01-24 13:33:10,934] [INFO] Running command: blastn -query GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06d32f2-29c3-43f9-aa20-0aa3a3ae43b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,755] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,758] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:11,758] [INFO] Target genome list was writen to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:11,770] [INFO] Task started: fastANI
[2024-01-24 13:33:11,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg223ce5e3-e1aa-44a0-8965-49abc10ac5ce/GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna.gz --refList GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:19,873] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:19,881] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:19,881] [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
GCF_000340375.1	s__Eggerthia catenaformis	99.9999	637	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Eggerthia	95.0	98.71	98.60	0.88	0.87	3	conclusive
GCF_009767585.1	s__Coprobacillus cateniformis	77.8045	83	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus	95.0	99.28	99.05	0.92	0.87	12	-
GCF_000702165.1	s__Sharpea azabuensis	77.5323	97	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Sharpea	95.0	98.40	97.32	0.90	0.79	46	-
GCF_000702065.1	s__Kandleria vitulina	77.0778	107	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Kandleria	95.0	98.93	98.27	0.93	0.86	20	-
GCF_004168205.1	s__Catenibacterium sp000437715	77.0223	88	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCF_000173795.1	s__Catenibacterium mitsuokai	76.9497	95	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	-
GCA_910588075.1	s__MGBC163490 sp910588075	76.9261	89	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540685.1	s__Catenibacterium sp900540685	76.7614	87	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCA_900540665.1	s__Catenibacterium sp900540665	76.6342	84	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	-
GCF_000455285.1	s__Stoquefichus massiliensis	76.5562	113	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003024685.1	s__Faecalibacillus intestinalis	76.5231	78	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCF_016901755.1	s__Faecalibacillus spiroforme_A	76.222	60	644	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:19,883] [INFO] GTDB search result was written to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:19,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:19,886] [INFO] DFAST_QC result json was written to GCF_000340375.1_Lact_cate_OT_569_V1_genomic.fna/dqc_result.json
[2024-01-24 13:33:19,886] [INFO] DFAST_QC completed!
[2024-01-24 13:33:19,886] [INFO] Total running time: 0h0m39s