[2023-06-17 12:24:35,137] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:35,141] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:35,141] [INFO] DQC Reference Directory: /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference
[2023-06-17 12:24:36,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:36,552] [INFO] Task started: Prodigal
[2023-06-17 12:24:36,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg60362fd5-cb02-4989-bf34-a92debc39c03/GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna.gz | prodigal -d GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/cds.fna -a GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:39,975] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:39,976] [INFO] Task started: HMMsearch
[2023-06-17 12:24:39,976] [INFO] Running command: hmmsearch --tblout GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/reference_markers.hmm GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:40,200] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:40,202] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60362fd5-cb02-4989-bf34-a92debc39c03/GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna.gz]
[2023-06-17 12:24:40,226] [INFO] Query marker FASTA was written to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/markers.fasta
[2023-06-17 12:24:40,227] [INFO] Task started: Blastn
[2023-06-17 12:24:40,227] [INFO] Running command: blastn -query GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/reference_markers.fasta -out GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:40,882] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:40,887] [INFO] Selected 6 target genomes.
[2023-06-17 12:24:40,888] [INFO] Target genome list was writen to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/target_genomes.txt
[2023-06-17 12:24:40,890] [INFO] Task started: fastANI
[2023-06-17 12:24:40,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg60362fd5-cb02-4989-bf34-a92debc39c03/GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna.gz --refList GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/target_genomes.txt --output GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:24:43,737] [INFO] Task succeeded: fastANI
[2023-06-17 12:24:43,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:24:43,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:24:43,746] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 12:24:43,746] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 12:24:43,746] [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	95.7244	451	521	95	conclusive
Veillonella infantium	strain=T11011-4	GCA_002959895.1	1911679	1911679	type	True	94.1952	454	521	95	below_threshold
Veillonella dispar	strain=ATCC 17748	GCA_000160015.1	39778	39778	suspected-type	True	92.5539	463	521	95	below_threshold
Veillonella dispar	strain=NCTC11831	GCA_900637515.1	39778	39778	suspected-type	True	92.4982	465	521	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_002959775.1	423477	423477	type	True	89.1096	441	521	95	below_threshold
Veillonella rogosae	strain=JCM 15642	GCA_001312485.1	423477	423477	type	True	88.9769	431	521	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:24:43,748] [INFO] DFAST Taxonomy check result was written to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/tc_result.tsv
[2023-06-17 12:24:43,749] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:24:43,749] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:24:43,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/checkm_data
[2023-06-17 12:24:43,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:24:43,778] [INFO] Task started: CheckM
[2023-06-17 12:24:43,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/checkm_input GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/checkm_result
[2023-06-17 12:25:02,106] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:02,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.76%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:02,138] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:02,138] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:02,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/markers.fasta)
[2023-06-17 12:25:02,139] [INFO] Task started: Blastn
[2023-06-17 12:25:02,139] [INFO] Running command: blastn -query GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/markers.fasta -db /var/lib/cwl/stg1580a8c3-81e5-46f0-b2ab-c9fd5d24e3c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:02,899] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:02,903] [INFO] Selected 11 target genomes.
[2023-06-17 12:25:02,904] [INFO] Target genome list was writen to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:02,912] [INFO] Task started: fastANI
[2023-06-17 12:25:02,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg60362fd5-cb02-4989-bf34-a92debc39c03/GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna.gz --refList GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/target_genomes_gtdb.txt --output GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:07,377] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:07,388] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:25:07,388] [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	95.7244	451	521	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_002959895.1	s__Veillonella infantium	94.1952	454	521	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	95.95	95.95	0.93	0.93	2	-
GCA_900766125.1	s__Veillonella sp900766125	94.1132	295	521	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_003463825.1	s__Veillonella sp003463825	93.7415	436	521	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_900552715.1	s__Veillonella sp900552715	92.5597	386	521	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_900637515.1	s__Veillonella dispar	92.4982	465	521	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.54	95.48	0.96	0.91	7	-
GCA_900545205.1	s__Veillonella sp900545205	92.4636	391	521	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	91.7168	387	521	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	91.4325	237	521	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	91.4051	389	521	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	89.1096	441	521	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella	95.0	96.92	95.91	0.92	0.87	12	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:07,406] [INFO] GTDB search result was written to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:07,407] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:07,412] [INFO] DFAST_QC result json was written to GCA_905201765.1_ERR414283-mag-bin.4_genomic.fna/dqc_result.json
[2023-06-17 12:25:07,413] [INFO] DFAST_QC completed!
[2023-06-17 12:25:07,414] [INFO] Total running time: 0h0m32s