[2024-01-25 18:28:50,814] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference
[2024-01-25 18:28:51,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,976] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f03d28e-fec4-4337-be65-63f65cb8b2fd/GCF_003992065.1_ASM399206v1_genomic.fna.gz | prodigal -d GCF_003992065.1_ASM399206v1_genomic.fna/cds.fna -a GCF_003992065.1_ASM399206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:56,456] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:56,456] [INFO] Task started: HMMsearch
[2024-01-25 18:28:56,456] [INFO] Running command: hmmsearch --tblout GCF_003992065.1_ASM399206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/reference_markers.hmm GCF_003992065.1_ASM399206v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:56,643] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:56,644] [INFO] Found 6/6 markers.
[2024-01-25 18:28:56,664] [INFO] Query marker FASTA was written to GCF_003992065.1_ASM399206v1_genomic.fna/markers.fasta
[2024-01-25 18:28:56,665] [INFO] Task started: Blastn
[2024-01-25 18:28:56,665] [INFO] Running command: blastn -query GCF_003992065.1_ASM399206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/reference_markers.fasta -out GCF_003992065.1_ASM399206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:57,198] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:57,200] [INFO] Selected 11 target genomes.
[2024-01-25 18:28:57,200] [INFO] Target genome list was writen to GCF_003992065.1_ASM399206v1_genomic.fna/target_genomes.txt
[2024-01-25 18:28:57,205] [INFO] Task started: fastANI
[2024-01-25 18:28:57,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f03d28e-fec4-4337-be65-63f65cb8b2fd/GCF_003992065.1_ASM399206v1_genomic.fna.gz --refList GCF_003992065.1_ASM399206v1_genomic.fna/target_genomes.txt --output GCF_003992065.1_ASM399206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:02,609] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:02,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:02,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:02,616] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:29:02,616] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:02,616] [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 seminalis	strain=ADV4313-2	GCA_003992065.1	1502943	1502943	type	True	100.0	738	739	95	conclusive
Veillonella ratti	strain=ATCC 17746	GCA_003992115.1	103892	103892	suspected-type	True	87.1367	554	739	95	below_threshold
Veillonella criceti	strain=NCTC12020	GCA_900460315.1	103891	103891	type	True	80.5325	328	739	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	78.5974	71	739	95	below_threshold
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	78.2126	97	739	95	below_threshold
Veillonella magna	strain=DSM 19857	GCA_000428745.1	464322	464322	type	True	77.9863	168	739	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	77.9769	106	739	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	77.9226	106	739	95	below_threshold
Veillonella rodentium	strain=NCTC12018	GCA_900187285.1	248315	248315	type	True	77.4667	115	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:02,618] [INFO] DFAST Taxonomy check result was written to GCF_003992065.1_ASM399206v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:02,618] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:02,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:02,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/checkm_data
[2024-01-25 18:29:02,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:02,644] [INFO] Task started: CheckM
[2024-01-25 18:29:02,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992065.1_ASM399206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992065.1_ASM399206v1_genomic.fna/checkm_input GCF_003992065.1_ASM399206v1_genomic.fna/checkm_result
[2024-01-25 18:29:21,442] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:21,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:21,458] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:21,458] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:21,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992065.1_ASM399206v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:21,459] [INFO] Task started: Blastn
[2024-01-25 18:29:21,459] [INFO] Running command: blastn -query GCF_003992065.1_ASM399206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadc8a5b-ed54-45f2-8e76-702e62a3202c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992065.1_ASM399206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:22,221] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:22,224] [INFO] Selected 9 target genomes.
[2024-01-25 18:29:22,224] [INFO] Target genome list was writen to GCF_003992065.1_ASM399206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:22,230] [INFO] Task started: fastANI
[2024-01-25 18:29:22,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f03d28e-fec4-4337-be65-63f65cb8b2fd/GCF_003992065.1_ASM399206v1_genomic.fna.gz --refList GCF_003992065.1_ASM399206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992065.1_ASM399206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:26,963] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:26,970] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:26,971] [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_003992065.1	s__Veillonella_A seminalis	100.0	738	739	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	conclusive
GCF_003992115.1	s__Veillonella_A ratti	87.1465	554	739	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_008679445.1	s__Veillonella_A sp000431435	87.1353	591	739	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	-
GCA_015058545.1	s__Veillonella_A sp015058545	86.5192	491	739	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_010093125.1	s__Veillonella_A sp010093125	80.5887	355	739	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	80.547	326	739	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_018364065.1	s__Veillonella_A sp018364065	79.6778	281	739	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:26,972] [INFO] GTDB search result was written to GCF_003992065.1_ASM399206v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:26,974] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:26,978] [INFO] DFAST_QC result json was written to GCF_003992065.1_ASM399206v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:26,979] [INFO] DFAST_QC completed!
[2024-01-25 18:29:26,979] [INFO] Total running time: 0h0m36s