[2024-01-24 12:16:03,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:03,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:03,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference
[2024-01-24 12:16:04,500] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:04,501] [INFO] Task started: Prodigal
[2024-01-24 12:16:04,501] [INFO] Running command: gunzip -c /var/lib/cwl/stg509d62db-ff7d-4621-bdef-48df06131bd9/GCF_002959915.1_ASM295991v1_genomic.fna.gz | prodigal -d GCF_002959915.1_ASM295991v1_genomic.fna/cds.fna -a GCF_002959915.1_ASM295991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:08,993] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:08,993] [INFO] Task started: HMMsearch
[2024-01-24 12:16:08,994] [INFO] Running command: hmmsearch --tblout GCF_002959915.1_ASM295991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/reference_markers.hmm GCF_002959915.1_ASM295991v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:09,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:09,240] [INFO] Found 6/6 markers.
[2024-01-24 12:16:09,261] [INFO] Query marker FASTA was written to GCF_002959915.1_ASM295991v1_genomic.fna/markers.fasta
[2024-01-24 12:16:09,261] [INFO] Task started: Blastn
[2024-01-24 12:16:09,261] [INFO] Running command: blastn -query GCF_002959915.1_ASM295991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/reference_markers.fasta -out GCF_002959915.1_ASM295991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:09,840] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:09,844] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:09,844] [INFO] Target genome list was writen to GCF_002959915.1_ASM295991v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:09,854] [INFO] Task started: fastANI
[2024-01-24 12:16:09,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg509d62db-ff7d-4621-bdef-48df06131bd9/GCF_002959915.1_ASM295991v1_genomic.fna.gz --refList GCF_002959915.1_ASM295991v1_genomic.fna/target_genomes.txt --output GCF_002959915.1_ASM295991v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:14,430] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:14,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:14,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:14,444] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:16:14,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:14,444] [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 atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	100.0	671	673	95	conclusive
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	99.9937	667	673	95	conclusive
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	99.9498	645	673	95	conclusive
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	88.8434	552	673	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	84.3093	433	673	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	84.1958	449	673	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	83.9247	440	673	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	83.1009	403	673	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	82.7679	416	673	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	81.1086	337	673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:14,446] [INFO] DFAST Taxonomy check result was written to GCF_002959915.1_ASM295991v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:14,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:14,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:14,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/checkm_data
[2024-01-24 12:16:14,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:14,469] [INFO] Task started: CheckM
[2024-01-24 12:16:14,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002959915.1_ASM295991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002959915.1_ASM295991v1_genomic.fna/checkm_input GCF_002959915.1_ASM295991v1_genomic.fna/checkm_result
[2024-01-24 12:16:34,845] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:34,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:34,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:34,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:34,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002959915.1_ASM295991v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:34,876] [INFO] Task started: Blastn
[2024-01-24 12:16:34,876] [INFO] Running command: blastn -query GCF_002959915.1_ASM295991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fdf393-ffeb-4626-8a74-4adafe5e9058/dqc_reference/reference_markers_gtdb.fasta -out GCF_002959915.1_ASM295991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:35,667] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:35,671] [INFO] Selected 13 target genomes.
[2024-01-24 12:16:35,671] [INFO] Target genome list was writen to GCF_002959915.1_ASM295991v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:35,684] [INFO] Task started: fastANI
[2024-01-24 12:16:35,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg509d62db-ff7d-4621-bdef-48df06131bd9/GCF_002959915.1_ASM295991v1_genomic.fna.gz --refList GCF_002959915.1_ASM295991v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002959915.1_ASM295991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:41,501] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:41,516] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:41,516] [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_002959915.1	s__Veillonella atypica	100.0	669	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	conclusive
GCA_905214495.1	s__Veillonella sp905214495	94.347	460	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_001078375.1	s__Veillonella tobetsuensis	88.8434	552	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCA_900550175.1	s__Veillonella sp900550175	84.3596	319	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	-
GCF_002959755.1	s__Veillonella sp002959755	84.0251	437	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	84.0233	305	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_002959895.1	s__Veillonella infantium	83.9457	439	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCA_900538355.1	s__Veillonella sp900538355	83.8	425	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	82.9102	248	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_000024945.1	s__Veillonella parvula	82.7813	415	673	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_905209685.1	s__Veillonella sp905209685	82.7357	332	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_900556785.1	s__Veillonella sp900556785	82.5914	302	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_003992125.1	s__Veillonella caviae	81.1086	337	673	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:41,518] [INFO] GTDB search result was written to GCF_002959915.1_ASM295991v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:41,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:41,522] [INFO] DFAST_QC result json was written to GCF_002959915.1_ASM295991v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:41,522] [INFO] DFAST_QC completed!
[2024-01-24 12:16:41,522] [INFO] Total running time: 0h0m38s