[2023-06-19 08:45:48,899] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:48,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:48,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference
[2023-06-19 08:45:50,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:50,168] [INFO] Task started: Prodigal
[2023-06-19 08:45:50,168] [INFO] Running command: gunzip -c /var/lib/cwl/stgee39215d-9d3b-477b-a2c1-85da0d4ece04/GCA_018059065.1_ASM1805906v1_genomic.fna.gz | prodigal -d GCA_018059065.1_ASM1805906v1_genomic.fna/cds.fna -a GCA_018059065.1_ASM1805906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:54,076] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:54,077] [INFO] Task started: HMMsearch
[2023-06-19 08:45:54,077] [INFO] Running command: hmmsearch --tblout GCA_018059065.1_ASM1805906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/reference_markers.hmm GCA_018059065.1_ASM1805906v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:54,276] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:54,278] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgee39215d-9d3b-477b-a2c1-85da0d4ece04/GCA_018059065.1_ASM1805906v1_genomic.fna.gz]
[2023-06-19 08:45:54,301] [INFO] Query marker FASTA was written to GCA_018059065.1_ASM1805906v1_genomic.fna/markers.fasta
[2023-06-19 08:45:54,301] [INFO] Task started: Blastn
[2023-06-19 08:45:54,301] [INFO] Running command: blastn -query GCA_018059065.1_ASM1805906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/reference_markers.fasta -out GCA_018059065.1_ASM1805906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:54,885] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:54,889] [INFO] Selected 11 target genomes.
[2023-06-19 08:45:54,889] [INFO] Target genome list was writen to GCA_018059065.1_ASM1805906v1_genomic.fna/target_genomes.txt
[2023-06-19 08:45:54,895] [INFO] Task started: fastANI
[2023-06-19 08:45:54,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgee39215d-9d3b-477b-a2c1-85da0d4ece04/GCA_018059065.1_ASM1805906v1_genomic.fna.gz --refList GCA_018059065.1_ASM1805906v1_genomic.fna/target_genomes.txt --output GCA_018059065.1_ASM1805906v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:46:02,302] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:02,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:46:02,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:46:02,313] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 08:46:02,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 08:46:02,313] [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
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	99.4171	344	353	95	conclusive
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	77.7646	56	353	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.7429	73	353	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.6985	81	353	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_902167245.1	881	881	type	True	77.4827	74	353	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	77.4468	75	353	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:46:02,316] [INFO] DFAST Taxonomy check result was written to GCA_018059065.1_ASM1805906v1_genomic.fna/tc_result.tsv
[2023-06-19 08:46:02,316] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:46:02,317] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:46:02,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/checkm_data
[2023-06-19 08:46:02,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:46:02,344] [INFO] Task started: CheckM
[2023-06-19 08:46:02,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018059065.1_ASM1805906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018059065.1_ASM1805906v1_genomic.fna/checkm_input GCA_018059065.1_ASM1805906v1_genomic.fna/checkm_result
[2023-06-19 08:46:21,122] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:21,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.39%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:21,160] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:21,161] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:21,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018059065.1_ASM1805906v1_genomic.fna/markers.fasta)
[2023-06-19 08:46:21,162] [INFO] Task started: Blastn
[2023-06-19 08:46:21,162] [INFO] Running command: blastn -query GCA_018059065.1_ASM1805906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10d4d28d-8fa4-46b2-8fb8-d009383f6fef/dqc_reference/reference_markers_gtdb.fasta -out GCA_018059065.1_ASM1805906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:21,930] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:21,934] [INFO] Selected 6 target genomes.
[2023-06-19 08:46:21,934] [INFO] Target genome list was writen to GCA_018059065.1_ASM1805906v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:21,938] [INFO] Task started: fastANI
[2023-06-19 08:46:21,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgee39215d-9d3b-477b-a2c1-85da0d4ece04/GCA_018059065.1_ASM1805906v1_genomic.fna.gz --refList GCA_018059065.1_ASM1805906v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018059065.1_ASM1805906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:25,075] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:25,087] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:46:25,088] [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_000701705.1	s__Bilophila wadsworthia	99.4171	344	353	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.41	97.08	0.87	0.83	9	conclusive
GCA_900550745.1	s__Bilophila sp900550745	92.7106	256	353	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	97.48	97.27	0.74	0.71	3	-
GCA_900553145.1	s__Bilophila sp900553145	90.7948	306	353	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373525.1	s__Bilophila sp902373525	86.1093	264	353	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	98.79	98.79	0.94	0.94	2	-
GCA_019114025.1	s__Bilophila faecipullorum	82.6598	219	353	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila	95.0	99.16	98.64	0.81	0.70	3	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:25,090] [INFO] GTDB search result was written to GCA_018059065.1_ASM1805906v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:25,091] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:25,094] [INFO] DFAST_QC result json was written to GCA_018059065.1_ASM1805906v1_genomic.fna/dqc_result.json
[2023-06-19 08:46:25,094] [INFO] DFAST_QC completed!
[2023-06-19 08:46:25,094] [INFO] Total running time: 0h0m36s