[2024-01-24 13:32:33,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:33,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:33,726] [INFO] DQC Reference Directory: /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference
[2024-01-24 13:32:35,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,109] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,110] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ecc45e8-982d-434c-88bf-6830ad74e177/GCF_002959775.1_ASM295977v1_genomic.fna.gz | prodigal -d GCF_002959775.1_ASM295977v1_genomic.fna/cds.fna -a GCF_002959775.1_ASM295977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:40,036] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:40,036] [INFO] Task started: HMMsearch
[2024-01-24 13:32:40,036] [INFO] Running command: hmmsearch --tblout GCF_002959775.1_ASM295977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/reference_markers.hmm GCF_002959775.1_ASM295977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:40,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:40,379] [INFO] Found 6/6 markers.
[2024-01-24 13:32:40,401] [INFO] Query marker FASTA was written to GCF_002959775.1_ASM295977v1_genomic.fna/markers.fasta
[2024-01-24 13:32:40,402] [INFO] Task started: Blastn
[2024-01-24 13:32:40,402] [INFO] Running command: blastn -query GCF_002959775.1_ASM295977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/reference_markers.fasta -out GCF_002959775.1_ASM295977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,011] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:41,011] [INFO] Target genome list was writen to GCF_002959775.1_ASM295977v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,015] [INFO] Task started: fastANI
[2024-01-24 13:32:41,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ecc45e8-982d-434c-88bf-6830ad74e177/GCF_002959775.1_ASM295977v1_genomic.fna.gz --refList GCF_002959775.1_ASM295977v1_genomic.fna/target_genomes.txt --output GCF_002959775.1_ASM295977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:45,731] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:45,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:45,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:45,740] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:45,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:45,740] [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 rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	100.0	721	722	95	conclusive
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	99.7846	682	722	95	conclusive
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	90.2776	600	722	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	89.9179	593	722	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	89.2027	599	722	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	88.9815	611	722	95	below_threshold
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	87.217	578	722	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	87.1701	576	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,742] [INFO] DFAST Taxonomy check result was written to GCF_002959775.1_ASM295977v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:45,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:45,743] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:45,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/checkm_data
[2024-01-24 13:32:45,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:45,773] [INFO] Task started: CheckM
[2024-01-24 13:32:45,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002959775.1_ASM295977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002959775.1_ASM295977v1_genomic.fna/checkm_input GCF_002959775.1_ASM295977v1_genomic.fna/checkm_result
[2024-01-24 13:33:08,719] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:08,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,751] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:08,752] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:08,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002959775.1_ASM295977v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:08,752] [INFO] Task started: Blastn
[2024-01-24 13:33:08,753] [INFO] Running command: blastn -query GCF_002959775.1_ASM295977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7677ea3-96fb-4ea2-8b19-673ad4b1d034/dqc_reference/reference_markers_gtdb.fasta -out GCF_002959775.1_ASM295977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:09,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:09,771] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:09,771] [INFO] Target genome list was writen to GCF_002959775.1_ASM295977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:09,843] [INFO] Task started: fastANI
[2024-01-24 13:33:09,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ecc45e8-982d-434c-88bf-6830ad74e177/GCF_002959775.1_ASM295977v1_genomic.fna.gz --refList GCF_002959775.1_ASM295977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002959775.1_ASM295977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:16,344] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:16,357] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:16,358] [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_002959775.1	s__Veillonella rogosae	100.0	721	722	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	conclusive
GCA_900552445.1	s__Veillonella sp900552445	94.2889	300	722	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_013393365.1	s__Veillonella nakazawae	90.2911	598	722	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	89.9179	593	722	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_003463825.1	s__Veillonella sp003463825	89.5621	545	722	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_900550175.1	s__Veillonella sp900550175	89.226	437	722	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_900637515.1	s__Veillonella dispar	89.2198	600	722	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_900552715.1	s__Veillonella sp900552715	89.026	475	722	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	89.0191	606	722	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	89.0011	406	722	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	88.8675	492	722	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_900766125.1	s__Veillonella sp900766125	88.6944	331	722	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	87.9308	333	722	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	87.1701	576	722	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	98.96	96.87	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,360] [INFO] GTDB search result was written to GCF_002959775.1_ASM295977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:16,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:16,365] [INFO] DFAST_QC result json was written to GCF_002959775.1_ASM295977v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:16,365] [INFO] DFAST_QC completed!
[2024-01-24 13:33:16,365] [INFO] Total running time: 0h0m43s