[2023-06-19 08:35:04,499] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:35:04,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:35:04,501] [INFO] DQC Reference Directory: /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference
[2023-06-19 08:35:05,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:35:05,710] [INFO] Task started: Prodigal
[2023-06-19 08:35:05,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg94abfd23-fc6f-4b4d-9f7d-4717921d6a7d/GCA_018381565.1_ASM1838156v1_genomic.fna.gz | prodigal -d GCA_018381565.1_ASM1838156v1_genomic.fna/cds.fna -a GCA_018381565.1_ASM1838156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:35:10,032] [INFO] Task succeeded: Prodigal
[2023-06-19 08:35:10,033] [INFO] Task started: HMMsearch
[2023-06-19 08:35:10,033] [INFO] Running command: hmmsearch --tblout GCA_018381565.1_ASM1838156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/reference_markers.hmm GCA_018381565.1_ASM1838156v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:35:10,271] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:35:10,272] [INFO] Found 6/6 markers.
[2023-06-19 08:35:10,297] [INFO] Query marker FASTA was written to GCA_018381565.1_ASM1838156v1_genomic.fna/markers.fasta
[2023-06-19 08:35:10,298] [INFO] Task started: Blastn
[2023-06-19 08:35:10,298] [INFO] Running command: blastn -query GCA_018381565.1_ASM1838156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/reference_markers.fasta -out GCA_018381565.1_ASM1838156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:35:10,921] [INFO] Task succeeded: Blastn
[2023-06-19 08:35:10,926] [INFO] Selected 8 target genomes.
[2023-06-19 08:35:10,927] [INFO] Target genome list was writen to GCA_018381565.1_ASM1838156v1_genomic.fna/target_genomes.txt
[2023-06-19 08:35:10,928] [INFO] Task started: fastANI
[2023-06-19 08:35:10,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg94abfd23-fc6f-4b4d-9f7d-4717921d6a7d/GCA_018381565.1_ASM1838156v1_genomic.fna.gz --refList GCA_018381565.1_ASM1838156v1_genomic.fna/target_genomes.txt --output GCA_018381565.1_ASM1838156v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:35:15,062] [INFO] Task succeeded: fastANI
[2023-06-19 08:35:15,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:35:15,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:35:15,074] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:35:15,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:35:15,075] [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 nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	93.2451	594	673	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	93.0054	597	673	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	92.8713	596	673	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	92.2761	596	673	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	89.5421	587	673	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	89.397	568	673	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	86.8004	556	673	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	86.7026	567	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:35:15,076] [INFO] DFAST Taxonomy check result was written to GCA_018381565.1_ASM1838156v1_genomic.fna/tc_result.tsv
[2023-06-19 08:35:15,077] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:35:15,077] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:35:15,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/checkm_data
[2023-06-19 08:35:15,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:35:15,106] [INFO] Task started: CheckM
[2023-06-19 08:35:15,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018381565.1_ASM1838156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018381565.1_ASM1838156v1_genomic.fna/checkm_input GCA_018381565.1_ASM1838156v1_genomic.fna/checkm_result
[2023-06-19 08:35:35,956] [INFO] Task succeeded: CheckM
[2023-06-19 08:35:35,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:35:36,006] [INFO] ===== Completeness check finished =====
[2023-06-19 08:35:36,007] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:35:36,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018381565.1_ASM1838156v1_genomic.fna/markers.fasta)
[2023-06-19 08:35:36,008] [INFO] Task started: Blastn
[2023-06-19 08:35:36,008] [INFO] Running command: blastn -query GCA_018381565.1_ASM1838156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7ab21a9-3bf7-49e6-b9a9-09b0a4dd5865/dqc_reference/reference_markers_gtdb.fasta -out GCA_018381565.1_ASM1838156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:35:36,999] [INFO] Task succeeded: Blastn
[2023-06-19 08:35:37,004] [INFO] Selected 12 target genomes.
[2023-06-19 08:35:37,004] [INFO] Target genome list was writen to GCA_018381565.1_ASM1838156v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:35:37,005] [INFO] Task started: fastANI
[2023-06-19 08:35:37,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg94abfd23-fc6f-4b4d-9f7d-4717921d6a7d/GCA_018381565.1_ASM1838156v1_genomic.fna.gz --refList GCA_018381565.1_ASM1838156v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018381565.1_ASM1838156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:35:41,939] [INFO] Task succeeded: fastANI
[2023-06-19 08:35:41,950] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:35:41,951] [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_900550175.1	s__Veillonella sp900550175	97.7704	458	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.03	98.03	0.91	0.91	2	conclusive
GCF_003463825.1	s__Veillonella sp003463825	93.0189	548	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.70	95.41	0.92	0.86	3	-
GCF_900637515.1	s__Veillonella dispar	93.0054	597	673	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_900545205.1	s__Veillonella sp900545205	92.8088	497	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.54	95.18	0.86	0.80	3	-
GCA_900552715.1	s__Veillonella sp900552715	92.7291	483	673	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_002959755.1	s__Veillonella sp002959755	92.6734	591	673	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_900549845.1	s__Veillonella sp900549845	92.6723	410	673	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	92.6466	569	673	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	92.185	453	673	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_902834965.1	s__Veillonella sp902834965	91.8501	288	673	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_900765235.1	s__Veillonella sp900765235	91.6986	339	673	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_002959775.1	s__Veillonella rogosae	89.5421	587	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
--------------------------------------------------------------------------------
[2023-06-19 08:35:41,953] [INFO] GTDB search result was written to GCA_018381565.1_ASM1838156v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:35:41,955] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:35:41,961] [INFO] DFAST_QC result json was written to GCA_018381565.1_ASM1838156v1_genomic.fna/dqc_result.json
[2023-06-19 08:35:41,962] [INFO] DFAST_QC completed!
[2023-06-19 08:35:41,962] [INFO] Total running time: 0h0m37s