[2024-01-25 18:52:20,731] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:20,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:20,743] [INFO] DQC Reference Directory: /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference
[2024-01-25 18:52:21,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:21,889] [INFO] Task started: Prodigal
[2024-01-25 18:52:21,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgc55e99fb-7fb8-48c9-8e97-2c30fd43f441/GCF_020687175.1_ASM2068717v1_genomic.fna.gz | prodigal -d GCF_020687175.1_ASM2068717v1_genomic.fna/cds.fna -a GCF_020687175.1_ASM2068717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:25,700] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:25,701] [INFO] Task started: HMMsearch
[2024-01-25 18:52:25,701] [INFO] Running command: hmmsearch --tblout GCF_020687175.1_ASM2068717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/reference_markers.hmm GCF_020687175.1_ASM2068717v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:25,900] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:25,901] [INFO] Found 6/6 markers.
[2024-01-25 18:52:25,920] [INFO] Query marker FASTA was written to GCF_020687175.1_ASM2068717v1_genomic.fna/markers.fasta
[2024-01-25 18:52:25,921] [INFO] Task started: Blastn
[2024-01-25 18:52:25,921] [INFO] Running command: blastn -query GCF_020687175.1_ASM2068717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/reference_markers.fasta -out GCF_020687175.1_ASM2068717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:26,453] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:26,455] [INFO] Selected 8 target genomes.
[2024-01-25 18:52:26,455] [INFO] Target genome list was writen to GCF_020687175.1_ASM2068717v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:26,456] [INFO] Task started: fastANI
[2024-01-25 18:52:26,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55e99fb-7fb8-48c9-8e97-2c30fd43f441/GCF_020687175.1_ASM2068717v1_genomic.fna.gz --refList GCF_020687175.1_ASM2068717v1_genomic.fna/target_genomes.txt --output GCF_020687175.1_ASM2068717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:30,309] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:30,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:30,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:30,316] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:52:30,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:52:30,316] [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 dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	94.9656	601	669	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	94.8495	607	669	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	93.5163	600	669	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	93.0089	601	669	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	89.1049	586	669	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	89.0794	559	669	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	86.8259	549	669	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	86.7895	559	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:30,318] [INFO] DFAST Taxonomy check result was written to GCF_020687175.1_ASM2068717v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:30,318] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:30,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:30,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/checkm_data
[2024-01-25 18:52:30,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:30,342] [INFO] Task started: CheckM
[2024-01-25 18:52:30,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020687175.1_ASM2068717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020687175.1_ASM2068717v1_genomic.fna/checkm_input GCF_020687175.1_ASM2068717v1_genomic.fna/checkm_result
[2024-01-25 18:52:47,293] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:47,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:47,312] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:47,312] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:47,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020687175.1_ASM2068717v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:47,313] [INFO] Task started: Blastn
[2024-01-25 18:52:47,313] [INFO] Running command: blastn -query GCF_020687175.1_ASM2068717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6f4af8f-6cf1-4a05-8890-7b02305dcdf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_020687175.1_ASM2068717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:48,034] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:48,036] [INFO] Selected 14 target genomes.
[2024-01-25 18:52:48,037] [INFO] Target genome list was writen to GCF_020687175.1_ASM2068717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:48,042] [INFO] Task started: fastANI
[2024-01-25 18:52:48,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgc55e99fb-7fb8-48c9-8e97-2c30fd43f441/GCF_020687175.1_ASM2068717v1_genomic.fna.gz --refList GCF_020687175.1_ASM2068717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020687175.1_ASM2068717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:53,843] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:53,851] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:52:53,852] [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_900637515.1	s__Veillonella dispar	94.8791	606	669	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCF_002959755.1	s__Veillonella sp002959755	94.5265	597	669	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_900545205.1	s__Veillonella sp900545205	94.4651	496	669	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_905209685.1	s__Veillonella sp905209685	94.3208	467	669	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_900549845.1	s__Veillonella sp900549845	94.3169	401	669	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_900552715.1	s__Veillonella sp900552715	94.2371	480	669	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_003463825.1	s__Veillonella sp003463825	94.2175	548	669	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.70	95.41	0.92	0.86	3	-
GCA_900765235.1	s__Veillonella sp900765235	93.8973	336	669	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	93.8167	587	669	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_900766125.1	s__Veillonella sp900766125	93.5353	332	669	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_013393365.1	s__Veillonella nakazawae	93.5306	599	669	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_002959895.1	s__Veillonella infantium	93.0526	599	669	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_900550175.1	s__Veillonella sp900550175	92.4929	423	669	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_002959775.1	s__Veillonella rogosae	89.0933	587	669	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:53,853] [INFO] GTDB search result was written to GCF_020687175.1_ASM2068717v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:53,854] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:53,856] [INFO] DFAST_QC result json was written to GCF_020687175.1_ASM2068717v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:53,856] [INFO] DFAST_QC completed!
[2024-01-25 18:52:53,856] [INFO] Total running time: 0h0m33s