[2024-01-24 15:19:04,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,446] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference
[2024-01-24 15:19:05,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,712] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,713] [INFO] Running command: gunzip -c /var/lib/cwl/stge4478a16-1a77-433c-be29-bd75e024e92e/GCF_003992125.1_ASM399212v1_genomic.fna.gz | prodigal -d GCF_003992125.1_ASM399212v1_genomic.fna/cds.fna -a GCF_003992125.1_ASM399212v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:09,817] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:09,818] [INFO] Task started: HMMsearch
[2024-01-24 15:19:09,818] [INFO] Running command: hmmsearch --tblout GCF_003992125.1_ASM399212v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/reference_markers.hmm GCF_003992125.1_ASM399212v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:10,040] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:10,042] [INFO] Found 6/6 markers.
[2024-01-24 15:19:10,067] [INFO] Query marker FASTA was written to GCF_003992125.1_ASM399212v1_genomic.fna/markers.fasta
[2024-01-24 15:19:10,068] [INFO] Task started: Blastn
[2024-01-24 15:19:10,068] [INFO] Running command: blastn -query GCF_003992125.1_ASM399212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/reference_markers.fasta -out GCF_003992125.1_ASM399212v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:10,656] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:10,660] [INFO] Selected 14 target genomes.
[2024-01-24 15:19:10,661] [INFO] Target genome list was writen to GCF_003992125.1_ASM399212v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:10,721] [INFO] Task started: fastANI
[2024-01-24 15:19:10,721] [INFO] Running command: fastANI --query /var/lib/cwl/stge4478a16-1a77-433c-be29-bd75e024e92e/GCF_003992125.1_ASM399212v1_genomic.fna.gz --refList GCF_003992125.1_ASM399212v1_genomic.fna/target_genomes.txt --output GCF_003992125.1_ASM399212v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:15,965] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:15,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:15,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:15,981] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:15,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:15,981] [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 caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	100.0	625	629	95	conclusive
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	81.078	342	629	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	81.0292	341	629	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	80.9409	332	629	95	below_threshold
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	80.823	332	629	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	80.7825	302	629	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	80.6997	303	629	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	80.6864	320	629	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	80.6863	329	629	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	80.5554	297	629	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	80.5371	310	629	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	80.1674	306	629	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	80.1541	299	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:15,983] [INFO] DFAST Taxonomy check result was written to GCF_003992125.1_ASM399212v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:15,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:15,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:15,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/checkm_data
[2024-01-24 15:19:15,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:16,005] [INFO] Task started: CheckM
[2024-01-24 15:19:16,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992125.1_ASM399212v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992125.1_ASM399212v1_genomic.fna/checkm_input GCF_003992125.1_ASM399212v1_genomic.fna/checkm_result
[2024-01-24 15:19:35,524] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:35,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:35,542] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:35,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:35,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992125.1_ASM399212v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:35,543] [INFO] Task started: Blastn
[2024-01-24 15:19:35,543] [INFO] Running command: blastn -query GCF_003992125.1_ASM399212v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2427d29-0ce4-4b8c-8574-5e471daeb522/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992125.1_ASM399212v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:36,403] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:36,407] [INFO] Selected 19 target genomes.
[2024-01-24 15:19:36,407] [INFO] Target genome list was writen to GCF_003992125.1_ASM399212v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:36,428] [INFO] Task started: fastANI
[2024-01-24 15:19:36,428] [INFO] Running command: fastANI --query /var/lib/cwl/stge4478a16-1a77-433c-be29-bd75e024e92e/GCF_003992125.1_ASM399212v1_genomic.fna.gz --refList GCF_003992125.1_ASM399212v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992125.1_ASM399212v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:43,065] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:43,079] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:43,079] [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_003992125.1	s__Veillonella caviae	100.0	625	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	conclusive
GCF_002959915.1	s__Veillonella atypica	81.0975	341	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCF_001078375.1	s__Veillonella tobetsuensis	80.8419	331	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCF_013393365.1	s__Veillonella nakazawae	80.7826	302	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	-
GCF_002959775.1	s__Veillonella rogosae	80.7202	302	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
GCF_900637515.1	s__Veillonella dispar	80.6863	329	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCA_900552445.1	s__Veillonella sp900552445	80.5487	173	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	97.10	0.94	0.94	2	-
GCF_002959895.1	s__Veillonella infantium	80.5371	310	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCF_002959755.1	s__Veillonella sp002959755	80.5053	315	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538355.1	s__Veillonella sp900538355	80.4395	310	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214495.1	s__Veillonella sp905214495	80.3407	268	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024945.1	s__Veillonella parvula	80.1541	299	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	98.96	96.87	0.98	0.94	4	-
GCA_900549845.1	s__Veillonella sp900549845	80.0461	226	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209685.1	s__Veillonella sp905209685	79.6448	245	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.07	95.07	0.78	0.78	2	-
GCA_018367495.1	s__Veillonella sp018367495	79.493	257	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902834965.1	s__Veillonella sp902834965	79.0835	160	629	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545795.1	s__Veillonella_A sp900545795	77.2649	100	629	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:43,081] [INFO] GTDB search result was written to GCF_003992125.1_ASM399212v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:43,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:43,085] [INFO] DFAST_QC result json was written to GCF_003992125.1_ASM399212v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:43,085] [INFO] DFAST_QC completed!
[2024-01-24 15:19:43,085] [INFO] Total running time: 0h0m39s