[2024-01-24 15:10:19,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference
[2024-01-24 15:10:22,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,721] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,721] [INFO] Running command: gunzip -c /var/lib/cwl/stga0c18634-2692-4035-a4ae-45112c992d9a/GCF_000318355.2_ASM31835v2_genomic.fna.gz | prodigal -d GCF_000318355.2_ASM31835v2_genomic.fna/cds.fna -a GCF_000318355.2_ASM31835v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:27,072] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:27,073] [INFO] Task started: HMMsearch
[2024-01-24 15:10:27,073] [INFO] Running command: hmmsearch --tblout GCF_000318355.2_ASM31835v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/reference_markers.hmm GCF_000318355.2_ASM31835v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:27,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:27,433] [INFO] Found 6/6 markers.
[2024-01-24 15:10:27,457] [INFO] Query marker FASTA was written to GCF_000318355.2_ASM31835v2_genomic.fna/markers.fasta
[2024-01-24 15:10:27,460] [INFO] Task started: Blastn
[2024-01-24 15:10:27,460] [INFO] Running command: blastn -query GCF_000318355.2_ASM31835v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/reference_markers.fasta -out GCF_000318355.2_ASM31835v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:30,085] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:30,092] [INFO] Selected 10 target genomes.
[2024-01-24 15:10:30,092] [INFO] Target genome list was writen to GCF_000318355.2_ASM31835v2_genomic.fna/target_genomes.txt
[2024-01-24 15:10:30,148] [INFO] Task started: fastANI
[2024-01-24 15:10:30,148] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c18634-2692-4035-a4ae-45112c992d9a/GCF_000318355.2_ASM31835v2_genomic.fna.gz --refList GCF_000318355.2_ASM31835v2_genomic.fna/target_genomes.txt --output GCF_000318355.2_ASM31835v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:34,690] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:34,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:34,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:34,705] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:10:34,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:34,706] [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=KON	GCA_000318355.2	39777	39777	type	True	100.0	644	645	95	conclusive
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	99.9915	645	645	95	conclusive
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	99.9912	645	645	95	conclusive
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	88.8997	538	645	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	84.1298	435	645	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	84.0536	431	645	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	83.9136	430	645	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	83.2887	395	645	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	82.7563	403	645	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	81.0667	330	645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:34,708] [INFO] DFAST Taxonomy check result was written to GCF_000318355.2_ASM31835v2_genomic.fna/tc_result.tsv
[2024-01-24 15:10:34,708] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:34,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:34,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/checkm_data
[2024-01-24 15:10:34,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:34,733] [INFO] Task started: CheckM
[2024-01-24 15:10:34,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000318355.2_ASM31835v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000318355.2_ASM31835v2_genomic.fna/checkm_input GCF_000318355.2_ASM31835v2_genomic.fna/checkm_result
[2024-01-24 15:10:59,782] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:59,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:59,823] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:59,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:59,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000318355.2_ASM31835v2_genomic.fna/markers.fasta)
[2024-01-24 15:10:59,824] [INFO] Task started: Blastn
[2024-01-24 15:10:59,824] [INFO] Running command: blastn -query GCF_000318355.2_ASM31835v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ad1ee3f-1f73-4107-88a3-fa1f095310f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000318355.2_ASM31835v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:00,816] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:00,820] [INFO] Selected 13 target genomes.
[2024-01-24 15:11:00,821] [INFO] Target genome list was writen to GCF_000318355.2_ASM31835v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:00,831] [INFO] Task started: fastANI
[2024-01-24 15:11:00,831] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c18634-2692-4035-a4ae-45112c992d9a/GCF_000318355.2_ASM31835v2_genomic.fna.gz --refList GCF_000318355.2_ASM31835v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000318355.2_ASM31835v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:06,525] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,536] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:06,536] [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	99.9915	645	645	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	94.3621	455	645	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	88.8997	538	645	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	84.1819	312	645	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_002959895.1	s__Veillonella infantium	83.9136	430	645	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	83.8662	437	645	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	83.8308	299	645	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	83.6232	422	645	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	82.7603	320	645	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.07	95.07	0.78	0.78	2	-
GCF_000024945.1	s__Veillonella parvula	82.7563	403	645	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_900556785.1	s__Veillonella sp900556785	82.7328	296	645	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	82.6559	248	645	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	81.0744	330	645	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 15:11:06,538] [INFO] GTDB search result was written to GCF_000318355.2_ASM31835v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:06,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:06,542] [INFO] DFAST_QC result json was written to GCF_000318355.2_ASM31835v2_genomic.fna/dqc_result.json
[2024-01-24 15:11:06,542] [INFO] DFAST_QC completed!
[2024-01-24 15:11:06,543] [INFO] Total running time: 0h0m47s