[2024-01-24 12:14:34,943] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference
[2024-01-24 12:14:36,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,297] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg88b3d793-3b65-4de3-9960-f14b059f4b35/GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna.gz | prodigal -d GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/cds.fna -a GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:40,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:40,539] [INFO] Task started: HMMsearch
[2024-01-24 12:14:40,539] [INFO] Running command: hmmsearch --tblout GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/reference_markers.hmm GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:40,795] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:40,797] [INFO] Found 6/6 markers.
[2024-01-24 12:14:40,825] [INFO] Query marker FASTA was written to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/markers.fasta
[2024-01-24 12:14:40,826] [INFO] Task started: Blastn
[2024-01-24 12:14:40,826] [INFO] Running command: blastn -query GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/markers.fasta -db /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/reference_markers.fasta -out GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:41,459] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:41,464] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:41,465] [INFO] Target genome list was writen to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/target_genomes.txt
[2024-01-24 12:14:41,471] [INFO] Task started: fastANI
[2024-01-24 12:14:41,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b3d793-3b65-4de3-9960-f14b059f4b35/GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna.gz --refList GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/target_genomes.txt --output GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:46,558] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:46,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:46,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:46,567] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:46,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:46,568] [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
Veillonella criceti	strain=NCTC12020	GCA_900460315.1	103891	103891	type	True	84.5964	543	699	95	below_threshold
Veillonella seminalis	strain=ADV4313-2	GCA_003992065.1	1502943	1502943	type	True	80.5462	340	699	95	below_threshold
Veillonella ratti	strain=ATCC 17746	GCA_003992115.1	103892	103892	suspected-type	True	80.1861	350	699	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	78.3553	118	699	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	78.0478	121	699	95	below_threshold
Veillonella denticariosi	strain=JCM 15641	GCA_002959855.1	419208	419208	type	True	78.011	77	699	95	below_threshold
Veillonella magna	strain=DSM 19857	GCA_000428745.1	464322	464322	type	True	78.005	132	699	95	below_threshold
Veillonella denticariosi	strain=JCM 15641	GCA_001312465.1	419208	419208	type	True	78.0018	73	699	95	below_threshold
Veillonella montpellierensis	strain=DSM 17217	GCA_000426745.1	187328	187328	type	True	77.4656	102	699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:46,569] [INFO] DFAST Taxonomy check result was written to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/tc_result.tsv
[2024-01-24 12:14:46,569] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:46,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:46,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/checkm_data
[2024-01-24 12:14:46,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:46,600] [INFO] Task started: CheckM
[2024-01-24 12:14:46,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/checkm_input GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/checkm_result
[2024-01-24 12:15:07,664] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:07,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,681] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:07,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:07,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/markers.fasta)
[2024-01-24 12:15:07,682] [INFO] Task started: Blastn
[2024-01-24 12:15:07,682] [INFO] Running command: blastn -query GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/markers.fasta -db /var/lib/cwl/stg72b92a24-c5c3-4598-b388-48f983b1eafa/dqc_reference/reference_markers_gtdb.fasta -out GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:08,508] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:08,512] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:08,512] [INFO] Target genome list was writen to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:08,520] [INFO] Task started: fastANI
[2024-01-24 12:15:08,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg88b3d793-3b65-4de3-9960-f14b059f4b35/GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna.gz --refList GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/target_genomes_gtdb.txt --output GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:13,158] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:13,167] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:13,167] [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_010093125.1	s__Veillonella_A sp010093125	86.3386	563	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460315.1	s__Veillonella_A criceti	84.5781	544	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992065.1	s__Veillonella_A seminalis	80.5442	341	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	99.33	98.86	0.95	0.92	5	-
GCA_008679445.1	s__Veillonella_A sp000431435	80.2145	345	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	99.32	99.06	0.94	0.85	7	-
GCF_003992115.1	s__Veillonella_A ratti	80.1854	350	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545795.1	s__Veillonella_A sp900545795	79.8863	309	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058545.1	s__Veillonella_A sp015058545	79.8049	302	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992315.1	s__F0422 sp003992315	78.1133	123	699	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__F0422	95.0	99.56	99.56	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:13,169] [INFO] GTDB search result was written to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:13,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:13,173] [INFO] DFAST_QC result json was written to GCF_943192895.1_Veillonella_sp_nov1_DSM110113_genomic.fna/dqc_result.json
[2024-01-24 12:15:13,173] [INFO] DFAST_QC completed!
[2024-01-24 12:15:13,173] [INFO] Total running time: 0h0m38s