[2023-06-18 18:31:03,928] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:03,930] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:03,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference
[2023-06-18 18:31:05,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:05,351] [INFO] Task started: Prodigal
[2023-06-18 18:31:05,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg240a8055-f491-46fc-934b-c7b3e1d62d82/GCA_018375655.1_ASM1837565v1_genomic.fna.gz | prodigal -d GCA_018375655.1_ASM1837565v1_genomic.fna/cds.fna -a GCA_018375655.1_ASM1837565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:09,866] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:09,867] [INFO] Task started: HMMsearch
[2023-06-18 18:31:09,867] [INFO] Running command: hmmsearch --tblout GCA_018375655.1_ASM1837565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/reference_markers.hmm GCA_018375655.1_ASM1837565v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:10,138] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:10,139] [INFO] Found 6/6 markers.
[2023-06-18 18:31:10,177] [INFO] Query marker FASTA was written to GCA_018375655.1_ASM1837565v1_genomic.fna/markers.fasta
[2023-06-18 18:31:10,177] [INFO] Task started: Blastn
[2023-06-18 18:31:10,178] [INFO] Running command: blastn -query GCA_018375655.1_ASM1837565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/reference_markers.fasta -out GCA_018375655.1_ASM1837565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:10,783] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:10,786] [INFO] Selected 6 target genomes.
[2023-06-18 18:31:10,787] [INFO] Target genome list was writen to GCA_018375655.1_ASM1837565v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:10,787] [INFO] Task started: fastANI
[2023-06-18 18:31:10,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg240a8055-f491-46fc-934b-c7b3e1d62d82/GCA_018375655.1_ASM1837565v1_genomic.fna.gz --refList GCA_018375655.1_ASM1837565v1_genomic.fna/target_genomes.txt --output GCA_018375655.1_ASM1837565v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:14,248] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:14,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:14,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:14,256] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 18:31:14,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 18:31:14,257] [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 nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	96.3597	607	672	95	conclusive
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	94.5355	610	672	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	93.8806	610	672	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	93.8264	610	672	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	90.2598	590	672	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	90.2151	571	672	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:14,259] [INFO] DFAST Taxonomy check result was written to GCA_018375655.1_ASM1837565v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:14,259] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:14,259] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:14,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/checkm_data
[2023-06-18 18:31:14,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:14,285] [INFO] Task started: CheckM
[2023-06-18 18:31:14,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018375655.1_ASM1837565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018375655.1_ASM1837565v1_genomic.fna/checkm_input GCA_018375655.1_ASM1837565v1_genomic.fna/checkm_result
[2023-06-18 18:31:35,433] [INFO] Task succeeded: CheckM
[2023-06-18 18:31:35,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:31:35,458] [INFO] ===== Completeness check finished =====
[2023-06-18 18:31:35,458] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:31:35,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018375655.1_ASM1837565v1_genomic.fna/markers.fasta)
[2023-06-18 18:31:35,459] [INFO] Task started: Blastn
[2023-06-18 18:31:35,459] [INFO] Running command: blastn -query GCA_018375655.1_ASM1837565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd48fde-8206-49a0-8733-6a2a8b267c0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018375655.1_ASM1837565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:36,314] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:36,319] [INFO] Selected 13 target genomes.
[2023-06-18 18:31:36,319] [INFO] Target genome list was writen to GCA_018375655.1_ASM1837565v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:31:36,320] [INFO] Task started: fastANI
[2023-06-18 18:31:36,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg240a8055-f491-46fc-934b-c7b3e1d62d82/GCA_018375655.1_ASM1837565v1_genomic.fna.gz --refList GCA_018375655.1_ASM1837565v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018375655.1_ASM1837565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:31:42,085] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:42,102] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:31:42,103] [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_013393365.1	s__Veillonella nakazawae	96.3597	607	672	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.23	95.05	0.93	0.87	33	conclusive
GCF_003463825.1	s__Veillonella sp003463825	94.6327	556	672	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_900766125.1	s__Veillonella sp900766125	94.5556	332	672	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_002959895.1	s__Veillonella infantium	94.5328	610	672	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_900637515.1	s__Veillonella dispar	93.8806	610	672	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	93.4042	606	672	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	93.1864	508	672	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_900550175.1	s__Veillonella sp900550175	93.0024	427	672	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.03	98.03	0.91	0.91	2	-
GCA_900552715.1	s__Veillonella sp900552715	92.902	482	672	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	92.2671	464	672	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	91.9962	281	672	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	91.8	477	672	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_002959775.1	s__Veillonella rogosae	90.266	589	672	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
--------------------------------------------------------------------------------
[2023-06-18 18:31:42,105] [INFO] GTDB search result was written to GCA_018375655.1_ASM1837565v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:31:42,105] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:31:42,109] [INFO] DFAST_QC result json was written to GCA_018375655.1_ASM1837565v1_genomic.fna/dqc_result.json
[2023-06-18 18:31:42,109] [INFO] DFAST_QC completed!
[2023-06-18 18:31:42,109] [INFO] Total running time: 0h0m38s