[2024-01-24 12:31:33,973] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,976] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference
[2024-01-24 12:31:35,166] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,167] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb5550bd-04f0-4aa0-b11d-a564ea16ba9f/GCF_002959855.1_ASM295985v1_genomic.fna.gz | prodigal -d GCF_002959855.1_ASM295985v1_genomic.fna/cds.fna -a GCF_002959855.1_ASM295985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:39,996] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:39,997] [INFO] Task started: HMMsearch
[2024-01-24 12:31:39,997] [INFO] Running command: hmmsearch --tblout GCF_002959855.1_ASM295985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/reference_markers.hmm GCF_002959855.1_ASM295985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:40,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:40,246] [INFO] Found 6/6 markers.
[2024-01-24 12:31:40,280] [INFO] Query marker FASTA was written to GCF_002959855.1_ASM295985v1_genomic.fna/markers.fasta
[2024-01-24 12:31:40,281] [INFO] Task started: Blastn
[2024-01-24 12:31:40,281] [INFO] Running command: blastn -query GCF_002959855.1_ASM295985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/reference_markers.fasta -out GCF_002959855.1_ASM295985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:40,872] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:40,877] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:40,877] [INFO] Target genome list was writen to GCF_002959855.1_ASM295985v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:41,530] [INFO] Task started: fastANI
[2024-01-24 12:31:41,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb5550bd-04f0-4aa0-b11d-a564ea16ba9f/GCF_002959855.1_ASM295985v1_genomic.fna.gz --refList GCF_002959855.1_ASM295985v1_genomic.fna/target_genomes.txt --output GCF_002959855.1_ASM295985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:45,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:45,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:45,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:45,736] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:31:45,736] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:45,736] [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 denticariosi	strain=JCM 15641	GCA_002959855.1	419208	419208	type	True	100.0	657	657	95	inconclusive
Veillonella denticariosi	strain=JCM 15641	GCA_001312465.1	419208	419208	type	True	99.7711	647	657	95	inconclusive
Veillonella rodentium	strain=NCTC12018	GCA_900187285.1	248315	248315	type	True	95.3044	596	657	95	inconclusive
Veillonella parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	82.0862	419	657	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	81.9697	417	657	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	81.6222	392	657	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	81.565	392	657	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	81.4614	392	657	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	81.1925	385	657	95	below_threshold
Veillonella magna	strain=DSM 19857	GCA_000428745.1	464322	464322	type	True	77.2713	84	657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:45,738] [INFO] DFAST Taxonomy check result was written to GCF_002959855.1_ASM295985v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:45,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:45,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:45,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/checkm_data
[2024-01-24 12:31:45,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:45,765] [INFO] Task started: CheckM
[2024-01-24 12:31:45,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002959855.1_ASM295985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002959855.1_ASM295985v1_genomic.fna/checkm_input GCF_002959855.1_ASM295985v1_genomic.fna/checkm_result
[2024-01-24 12:32:07,103] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:07,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:07,132] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:07,132] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:07,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002959855.1_ASM295985v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:07,134] [INFO] Task started: Blastn
[2024-01-24 12:32:07,134] [INFO] Running command: blastn -query GCF_002959855.1_ASM295985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg298be8e8-246f-4600-8e05-e5e1beed4d9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002959855.1_ASM295985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:07,973] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:07,976] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:07,976] [INFO] Target genome list was writen to GCF_002959855.1_ASM295985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:07,995] [INFO] Task started: fastANI
[2024-01-24 12:32:07,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb5550bd-04f0-4aa0-b11d-a564ea16ba9f/GCF_002959855.1_ASM295985v1_genomic.fna.gz --refList GCF_002959855.1_ASM295985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002959855.1_ASM295985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:14,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:14,034] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:14,035] [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_002959855.1	s__Veillonella denticariosi	100.0	657	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.3196	98.41	97.05	0.97	0.95	3	conclusive
GCF_900187285.1	s__Veillonella rodentium	95.2827	597	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.3196	N/A	N/A	N/A	N/A	1	-
GCF_902810435.1	s__Veillonella parvula_A	81.9685	422	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	96.42	95.83	0.92	0.86	54	-
GCF_000024945.1	s__Veillonella parvula	81.9583	418	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	98.96	96.87	0.98	0.94	4	-
GCF_900637515.1	s__Veillonella dispar	81.6222	392	657	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_013393365.1	s__Veillonella nakazawae	81.476	391	657	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	81.4614	392	657	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_002959775.1	s__Veillonella rogosae	81.1925	385	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
GCA_900757715.1	s__Veillonella sp900757715	81.0578	345	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.4547	97.81	97.81	0.74	0.74	2	-
GCA_900549845.1	s__Veillonella sp900549845	81.0552	287	657	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	81.0225	348	657	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	80.6883	299	657	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	80.4562	187	657	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_018367495.1	s__Veillonella sp018367495	80.2233	314	657	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	79.6497	230	657	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_000428745.1	s__Veillonella_A magna	77.2713	84	657	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	97.49	96.83	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:14,037] [INFO] GTDB search result was written to GCF_002959855.1_ASM295985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:14,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:14,041] [INFO] DFAST_QC result json was written to GCF_002959855.1_ASM295985v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:14,041] [INFO] DFAST_QC completed!
[2024-01-24 12:32:14,041] [INFO] Total running time: 0h0m40s