[2023-06-29 08:44:17,981] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:17,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:17,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference
[2023-06-29 08:44:19,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:19,289] [INFO] Task started: Prodigal
[2023-06-29 08:44:19,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg547c132a-8c59-4d75-abd3-743f10adcb59/GCA_015264635.1_ASM1526463v1_genomic.fna.gz | prodigal -d GCA_015264635.1_ASM1526463v1_genomic.fna/cds.fna -a GCA_015264635.1_ASM1526463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:22,139] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:22,140] [INFO] Task started: HMMsearch
[2023-06-29 08:44:22,140] [INFO] Running command: hmmsearch --tblout GCA_015264635.1_ASM1526463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/reference_markers.hmm GCA_015264635.1_ASM1526463v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:22,388] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:22,390] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg547c132a-8c59-4d75-abd3-743f10adcb59/GCA_015264635.1_ASM1526463v1_genomic.fna.gz]
[2023-06-29 08:44:22,411] [INFO] Query marker FASTA was written to GCA_015264635.1_ASM1526463v1_genomic.fna/markers.fasta
[2023-06-29 08:44:22,412] [INFO] Task started: Blastn
[2023-06-29 08:44:22,412] [INFO] Running command: blastn -query GCA_015264635.1_ASM1526463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/reference_markers.fasta -out GCA_015264635.1_ASM1526463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:22,917] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:22,922] [INFO] Selected 11 target genomes.
[2023-06-29 08:44:22,923] [INFO] Target genome list was writen to GCA_015264635.1_ASM1526463v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:22,925] [INFO] Task started: fastANI
[2023-06-29 08:44:22,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg547c132a-8c59-4d75-abd3-743f10adcb59/GCA_015264635.1_ASM1526463v1_genomic.fna.gz --refList GCA_015264635.1_ASM1526463v1_genomic.fna/target_genomes.txt --output GCA_015264635.1_ASM1526463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:44:26,678] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:26,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:44:26,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:44:26,692] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-06-29 08:44:26,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 08:44:26,692] [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 atypica	strain=ATCC 17744	GCA_002959915.1	39777	39777	type	True	97.3548	241	256	95	conclusive
Veillonella atypica	strain=NCTC11830	GCA_900460235.1	39777	39777	type	True	97.3517	241	256	95	conclusive
Veillonella atypica	strain=KON	GCA_000318355.2	39777	39777	type	True	97.2948	240	256	95	conclusive
Veillonella tobetsuensis	strain=ATCC BAA-2400	GCA_001078375.1	1110546	1110546	type	True	88.0858	234	256	95	below_threshold
Veillonella nakazawae	strain=T1-7	GCA_013393365.1	2682456	2682456	type	True	83.6171	176	256	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	83.255	177	256	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	83.213	176	256	95	below_threshold
Veillonella parvula	strain=DSM 2008	GCA_000024945.1	29466	29466	suspected-type	True	82.1321	167	256	95	below_threshold
Veillonella caviae	strain=DSM 20738	GCA_003992125.1	248316	248316	type	True	80.8411	147	256	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:44:26,694] [INFO] DFAST Taxonomy check result was written to GCA_015264635.1_ASM1526463v1_genomic.fna/tc_result.tsv
[2023-06-29 08:44:26,695] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:44:26,695] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:44:26,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/checkm_data
[2023-06-29 08:44:26,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:44:26,715] [INFO] Task started: CheckM
[2023-06-29 08:44:26,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015264635.1_ASM1526463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015264635.1_ASM1526463v1_genomic.fna/checkm_input GCA_015264635.1_ASM1526463v1_genomic.fna/checkm_result
[2023-06-29 08:44:43,207] [INFO] Task succeeded: CheckM
[2023-06-29 08:44:43,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:44:43,227] [INFO] ===== Completeness check finished =====
[2023-06-29 08:44:43,228] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:44:43,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015264635.1_ASM1526463v1_genomic.fna/markers.fasta)
[2023-06-29 08:44:43,228] [INFO] Task started: Blastn
[2023-06-29 08:44:43,229] [INFO] Running command: blastn -query GCA_015264635.1_ASM1526463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769467ad-a230-4ffa-b196-0af337581fd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_015264635.1_ASM1526463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:43,675] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:43,679] [INFO] Selected 14 target genomes.
[2023-06-29 08:44:43,679] [INFO] Target genome list was writen to GCA_015264635.1_ASM1526463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:44:43,700] [INFO] Task started: fastANI
[2023-06-29 08:44:43,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg547c132a-8c59-4d75-abd3-743f10adcb59/GCA_015264635.1_ASM1526463v1_genomic.fna.gz --refList GCA_015264635.1_ASM1526463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015264635.1_ASM1526463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:44:48,363] [INFO] Task succeeded: fastANI
[2023-06-29 08:44:48,375] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 08:44:48,375] [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_002959915.1	s__Veillonella atypica	97.3548	241	256	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	97.10	95.19	0.91	0.87	34	conclusive
GCA_905214495.1	s__Veillonella sp905214495	94.7134	187	256	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_001078375.1	s__Veillonella tobetsuensis	88.0858	234	256	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_900637515.1	s__Veillonella dispar	83.255	177	256	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	83.1274	178	256	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	82.3757	125	256	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	81.9877	151	256	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_900765235.1	s__Veillonella sp900765235	81.7483	117	256	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_902834965.1	s__Veillonella sp902834965	81.7273	91	256	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_003992125.1	s__Veillonella caviae	80.8411	147	256	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	98.44	98.44	0.87	0.87	2	-
GCA_009929605.1	s__Veillonella sp009929605	79.5902	88	256	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	99.43	99.31	0.85	0.82	7	-
--------------------------------------------------------------------------------
[2023-06-29 08:44:48,378] [INFO] GTDB search result was written to GCA_015264635.1_ASM1526463v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:44:48,378] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:44:48,382] [INFO] DFAST_QC result json was written to GCA_015264635.1_ASM1526463v1_genomic.fna/dqc_result.json
[2023-06-29 08:44:48,382] [INFO] DFAST_QC completed!
[2023-06-29 08:44:48,382] [INFO] Total running time: 0h0m30s