[2023-06-19 00:40:16,047] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:40:16,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:40:16,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference
[2023-06-19 00:40:17,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:40:17,309] [INFO] Task started: Prodigal
[2023-06-19 00:40:17,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9405a97-e34c-4aef-b2fe-d0d1c950ba10/GCA_018376995.1_ASM1837699v1_genomic.fna.gz | prodigal -d GCA_018376995.1_ASM1837699v1_genomic.fna/cds.fna -a GCA_018376995.1_ASM1837699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:40:21,890] [INFO] Task succeeded: Prodigal
[2023-06-19 00:40:21,890] [INFO] Task started: HMMsearch
[2023-06-19 00:40:21,890] [INFO] Running command: hmmsearch --tblout GCA_018376995.1_ASM1837699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/reference_markers.hmm GCA_018376995.1_ASM1837699v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:40:22,137] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:40:22,140] [INFO] Found 6/6 markers.
[2023-06-19 00:40:22,164] [INFO] Query marker FASTA was written to GCA_018376995.1_ASM1837699v1_genomic.fna/markers.fasta
[2023-06-19 00:40:22,165] [INFO] Task started: Blastn
[2023-06-19 00:40:22,165] [INFO] Running command: blastn -query GCA_018376995.1_ASM1837699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/reference_markers.fasta -out GCA_018376995.1_ASM1837699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:22,754] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:22,760] [INFO] Selected 8 target genomes.
[2023-06-19 00:40:22,760] [INFO] Target genome list was writen to GCA_018376995.1_ASM1837699v1_genomic.fna/target_genomes.txt
[2023-06-19 00:40:22,761] [INFO] Task started: fastANI
[2023-06-19 00:40:22,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9405a97-e34c-4aef-b2fe-d0d1c950ba10/GCA_018376995.1_ASM1837699v1_genomic.fna.gz --refList GCA_018376995.1_ASM1837699v1_genomic.fna/target_genomes.txt --output GCA_018376995.1_ASM1837699v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:40:26,598] [INFO] Task succeeded: fastANI
[2023-06-19 00:40:26,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:40:26,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:40:26,610] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 00:40:26,610] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 00:40:26,610] [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 parvula	strain=NCTC11810	GCA_900186885.1	29466	29466	suspected-type	True	95.7791	641	701	95	conclusive
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	95.7631	640	701	95	conclusive
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	87.2705	573	701	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	87.2577	574	701	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	87.2422	569	701	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	87.1981	563	701	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	87.109	556	701	95	below_threshold
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	86.8919	570	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:40:26,612] [INFO] DFAST Taxonomy check result was written to GCA_018376995.1_ASM1837699v1_genomic.fna/tc_result.tsv
[2023-06-19 00:40:26,613] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:40:26,613] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:40:26,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/checkm_data
[2023-06-19 00:40:26,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:40:26,644] [INFO] Task started: CheckM
[2023-06-19 00:40:26,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376995.1_ASM1837699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376995.1_ASM1837699v1_genomic.fna/checkm_input GCA_018376995.1_ASM1837699v1_genomic.fna/checkm_result
[2023-06-19 00:40:47,963] [INFO] Task succeeded: CheckM
[2023-06-19 00:40:47,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:40:48,031] [INFO] ===== Completeness check finished =====
[2023-06-19 00:40:48,031] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:40:48,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376995.1_ASM1837699v1_genomic.fna/markers.fasta)
[2023-06-19 00:40:48,032] [INFO] Task started: Blastn
[2023-06-19 00:40:48,032] [INFO] Running command: blastn -query GCA_018376995.1_ASM1837699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277bb4ad-f283-4c4f-a00a-6412f71fe73d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376995.1_ASM1837699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:48,882] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:48,890] [INFO] Selected 11 target genomes.
[2023-06-19 00:40:48,890] [INFO] Target genome list was writen to GCA_018376995.1_ASM1837699v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:40:48,891] [INFO] Task started: fastANI
[2023-06-19 00:40:48,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9405a97-e34c-4aef-b2fe-d0d1c950ba10/GCA_018376995.1_ASM1837699v1_genomic.fna.gz --refList GCA_018376995.1_ASM1837699v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376995.1_ASM1837699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:40:53,373] [INFO] Task succeeded: fastANI
[2023-06-19 00:40:53,389] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:40:53,389] [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_902810435.1	s__Veillonella parvula_A	96.3071	628	701	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.7953	96.42	95.83	0.92	0.86	54	conclusive
GCF_000024945.1	s__Veillonella parvula	95.7631	640	701	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_900757715.1	s__Veillonella sp900757715	94.2128	516	701	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_900556785.1	s__Veillonella sp900556785	87.9197	404	701	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	87.4524	317	701	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	87.3502	572	701	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	87.3258	393	701	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	87.2724	472	701	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_002959775.1	s__Veillonella rogosae	87.2705	573	701	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_902834965.1	s__Veillonella sp902834965	87.2291	272	701	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	86.8919	570	701	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-19 00:40:53,394] [INFO] GTDB search result was written to GCA_018376995.1_ASM1837699v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:40:53,395] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:40:53,403] [INFO] DFAST_QC result json was written to GCA_018376995.1_ASM1837699v1_genomic.fna/dqc_result.json
[2023-06-19 00:40:53,403] [INFO] DFAST_QC completed!
[2023-06-19 00:40:53,404] [INFO] Total running time: 0h0m37s