[2024-01-24 14:39:14,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,828] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference
[2024-01-24 14:39:16,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,067] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,067] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7a074a4-e773-4eea-9efa-3128324565c2/GCF_000428745.1_ASM42874v1_genomic.fna.gz | prodigal -d GCF_000428745.1_ASM42874v1_genomic.fna/cds.fna -a GCF_000428745.1_ASM42874v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:21,726] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:21,726] [INFO] Task started: HMMsearch
[2024-01-24 14:39:21,726] [INFO] Running command: hmmsearch --tblout GCF_000428745.1_ASM42874v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/reference_markers.hmm GCF_000428745.1_ASM42874v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:21,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:21,978] [INFO] Found 6/6 markers.
[2024-01-24 14:39:22,004] [INFO] Query marker FASTA was written to GCF_000428745.1_ASM42874v1_genomic.fna/markers.fasta
[2024-01-24 14:39:22,004] [INFO] Task started: Blastn
[2024-01-24 14:39:22,004] [INFO] Running command: blastn -query GCF_000428745.1_ASM42874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/reference_markers.fasta -out GCF_000428745.1_ASM42874v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:22,614] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:22,617] [INFO] Selected 12 target genomes.
[2024-01-24 14:39:22,617] [INFO] Target genome list was writen to GCF_000428745.1_ASM42874v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:22,623] [INFO] Task started: fastANI
[2024-01-24 14:39:22,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a074a4-e773-4eea-9efa-3128324565c2/GCF_000428745.1_ASM42874v1_genomic.fna.gz --refList GCF_000428745.1_ASM42874v1_genomic.fna/target_genomes.txt --output GCF_000428745.1_ASM42874v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:27,162] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:27,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:27,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:27,172] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:27,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:27,172] [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 magna	strain=DSM 19857	GCA_000428745.1	464322	464322	type	True	100.0	713	716	95	conclusive
Veillonella atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	78.3867	61	716	95	below_threshold
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	78.3665	62	716	95	below_threshold
Veillonella ratti	strain=ATCC 17746	GCA_003992115.1	103892	103892	suspected-type	True	78.2039	157	716	95	below_threshold
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	78.1657	60	716	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	78.0766	57	716	95	below_threshold
Veillonella criceti	strain=NCTC12020	GCA_900460315.1	103891	103891	type	True	77.9555	136	716	95	below_threshold
Veillonella seminalis	strain=ADV4313-2	GCA_003992065.1	1502943	1502943	type	True	77.9092	169	716	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	77.9009	68	716	95	below_threshold
Veillonella denticariosi	strain=JCM 15641	GCA_002959855.1	419208	419208	type	True	77.4954	75	716	95	below_threshold
Veillonella denticariosi	strain=JCM 15641	GCA_001312465.1	419208	419208	type	True	77.4712	72	716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:27,174] [INFO] DFAST Taxonomy check result was written to GCF_000428745.1_ASM42874v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:27,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:27,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:27,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/checkm_data
[2024-01-24 14:39:27,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:27,204] [INFO] Task started: CheckM
[2024-01-24 14:39:27,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428745.1_ASM42874v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428745.1_ASM42874v1_genomic.fna/checkm_input GCF_000428745.1_ASM42874v1_genomic.fna/checkm_result
[2024-01-24 14:39:50,905] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:50,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:50,927] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:50,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:50,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428745.1_ASM42874v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:50,928] [INFO] Task started: Blastn
[2024-01-24 14:39:50,928] [INFO] Running command: blastn -query GCF_000428745.1_ASM42874v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9928ac-9124-4a5d-878e-272f052ee57e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428745.1_ASM42874v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:51,764] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:51,767] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:51,767] [INFO] Target genome list was writen to GCF_000428745.1_ASM42874v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:51,791] [INFO] Task started: fastANI
[2024-01-24 14:39:51,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7a074a4-e773-4eea-9efa-3128324565c2/GCF_000428745.1_ASM42874v1_genomic.fna.gz --refList GCF_000428745.1_ASM42874v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428745.1_ASM42874v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:00,362] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:00,375] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:00,375] [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_000428745.1	s__Veillonella_A magna	100.0	713	716	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	conclusive
GCF_002959915.1	s__Veillonella atypica	78.3799	60	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	-
GCA_900765165.1	s__Veillonella_A sp900765165	78.2972	153	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	99.20	99.13	0.88	0.87	4	-
GCF_003992115.1	s__Veillonella_A ratti	78.2039	157	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078375.1	s__Veillonella tobetsuensis	78.1271	55	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.55	97.11	0.92	0.91	7	-
GCF_003992125.1	s__Veillonella caviae	78.0129	58	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	-
GCF_900460315.1	s__Veillonella_A criceti	77.9555	136	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008679445.1	s__Veillonella_A sp000431435	77.9512	169	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	99.32	99.06	0.94	0.85	7	-
GCA_900545205.1	s__Veillonella sp900545205	77.9264	61	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.54	95.18	0.86	0.80	3	-
GCF_002959895.1	s__Veillonella infantium	77.9225	65	716	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_003992065.1	s__Veillonella_A seminalis	77.9206	170	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	99.33	98.86	0.95	0.92	5	-
GCF_002959855.1	s__Veillonella denticariosi	77.4993	74	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.3196	98.41	97.05	0.97	0.95	3	-
GCA_015058545.1	s__Veillonella_A sp015058545	77.4737	135	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992135.1	s__F0422 sp003992135	77.1625	64	716	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__F0422	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:00,377] [INFO] GTDB search result was written to GCF_000428745.1_ASM42874v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:00,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:00,381] [INFO] DFAST_QC result json was written to GCF_000428745.1_ASM42874v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:00,381] [INFO] DFAST_QC completed!
[2024-01-24 14:40:00,381] [INFO] Total running time: 0h0m46s