[2023-06-28 23:45:30,992] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:45:30,995] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:45:30,995] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference
[2023-06-28 23:45:32,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:45:32,193] [INFO] Task started: Prodigal
[2023-06-28 23:45:32,193] [INFO] Running command: gunzip -c /var/lib/cwl/stgf062cbcd-0cdf-4cd0-a00b-284c7cf89ddc/GCA_027441045.1_ASM2744104v1_genomic.fna.gz | prodigal -d GCA_027441045.1_ASM2744104v1_genomic.fna/cds.fna -a GCA_027441045.1_ASM2744104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:45:37,650] [INFO] Task succeeded: Prodigal
[2023-06-28 23:45:37,651] [INFO] Task started: HMMsearch
[2023-06-28 23:45:37,651] [INFO] Running command: hmmsearch --tblout GCA_027441045.1_ASM2744104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/reference_markers.hmm GCA_027441045.1_ASM2744104v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:45:37,857] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:45:37,858] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf062cbcd-0cdf-4cd0-a00b-284c7cf89ddc/GCA_027441045.1_ASM2744104v1_genomic.fna.gz]
[2023-06-28 23:45:37,882] [INFO] Query marker FASTA was written to GCA_027441045.1_ASM2744104v1_genomic.fna/markers.fasta
[2023-06-28 23:45:37,882] [INFO] Task started: Blastn
[2023-06-28 23:45:37,882] [INFO] Running command: blastn -query GCA_027441045.1_ASM2744104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/reference_markers.fasta -out GCA_027441045.1_ASM2744104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:45:38,589] [INFO] Task succeeded: Blastn
[2023-06-28 23:45:38,594] [INFO] Selected 20 target genomes.
[2023-06-28 23:45:38,594] [INFO] Target genome list was writen to GCA_027441045.1_ASM2744104v1_genomic.fna/target_genomes.txt
[2023-06-28 23:45:38,617] [INFO] Task started: fastANI
[2023-06-28 23:45:38,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgf062cbcd-0cdf-4cd0-a00b-284c7cf89ddc/GCA_027441045.1_ASM2744104v1_genomic.fna.gz --refList GCA_027441045.1_ASM2744104v1_genomic.fna/target_genomes.txt --output GCA_027441045.1_ASM2744104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:45:50,435] [INFO] Task succeeded: fastANI
[2023-06-28 23:45:50,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:45:50,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:45:50,443] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:45:50,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:45:50,444] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.7792	52	547	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5013	52	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:45:50,446] [INFO] DFAST Taxonomy check result was written to GCA_027441045.1_ASM2744104v1_genomic.fna/tc_result.tsv
[2023-06-28 23:45:50,446] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:45:50,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:45:50,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/checkm_data
[2023-06-28 23:45:50,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:45:50,473] [INFO] Task started: CheckM
[2023-06-28 23:45:50,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027441045.1_ASM2744104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027441045.1_ASM2744104v1_genomic.fna/checkm_input GCA_027441045.1_ASM2744104v1_genomic.fna/checkm_result
[2023-06-28 23:46:12,489] [INFO] Task succeeded: CheckM
[2023-06-28 23:46:12,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:46:12,511] [INFO] ===== Completeness check finished =====
[2023-06-28 23:46:12,511] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:46:12,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027441045.1_ASM2744104v1_genomic.fna/markers.fasta)
[2023-06-28 23:46:12,512] [INFO] Task started: Blastn
[2023-06-28 23:46:12,512] [INFO] Running command: blastn -query GCA_027441045.1_ASM2744104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4e17445-e148-4b06-ba4c-438145a745fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_027441045.1_ASM2744104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:46:13,581] [INFO] Task succeeded: Blastn
[2023-06-28 23:46:13,586] [INFO] Selected 19 target genomes.
[2023-06-28 23:46:13,586] [INFO] Target genome list was writen to GCA_027441045.1_ASM2744104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:46:13,597] [INFO] Task started: fastANI
[2023-06-28 23:46:13,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf062cbcd-0cdf-4cd0-a00b-284c7cf89ddc/GCA_027441045.1_ASM2744104v1_genomic.fna.gz --refList GCA_027441045.1_ASM2744104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027441045.1_ASM2744104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:46:24,367] [INFO] Task succeeded: fastANI
[2023-06-28 23:46:24,376] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:46:24,376] [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
GCA_018971605.1	s__REEB76 sp018971605	78.0675	163	547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__REEB76;f__REEB76;g__REEB76	95.0	99.78	99.78	0.93	0.93	2	-
GCA_018971365.1	s__REEB76 sp018971365	77.942	171	547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__REEB76;f__REEB76;g__REEB76	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.7792	52	547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.5013	52	547	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:46:24,379] [INFO] GTDB search result was written to GCA_027441045.1_ASM2744104v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:46:24,380] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:46:24,382] [INFO] DFAST_QC result json was written to GCA_027441045.1_ASM2744104v1_genomic.fna/dqc_result.json
[2023-06-28 23:46:24,383] [INFO] DFAST_QC completed!
[2023-06-28 23:46:24,383] [INFO] Total running time: 0h0m53s