[2023-06-27 23:46:04,160] [INFO] DFAST_QC pipeline started.
[2023-06-27 23:46:04,162] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 23:46:04,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference
[2023-06-27 23:46:05,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 23:46:05,370] [INFO] Task started: Prodigal
[2023-06-27 23:46:05,370] [INFO] Running command: gunzip -c /var/lib/cwl/stg69de40bd-bcba-4cf8-81cc-6b1d05024782/GCA_002167765.1_ASM216776v1_genomic.fna.gz | prodigal -d GCA_002167765.1_ASM216776v1_genomic.fna/cds.fna -a GCA_002167765.1_ASM216776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 23:46:11,397] [INFO] Task succeeded: Prodigal
[2023-06-27 23:46:11,397] [INFO] Task started: HMMsearch
[2023-06-27 23:46:11,397] [INFO] Running command: hmmsearch --tblout GCA_002167765.1_ASM216776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/reference_markers.hmm GCA_002167765.1_ASM216776v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 23:46:11,579] [INFO] Task succeeded: HMMsearch
[2023-06-27 23:46:11,581] [INFO] Found 6/6 markers.
[2023-06-27 23:46:11,605] [INFO] Query marker FASTA was written to GCA_002167765.1_ASM216776v1_genomic.fna/markers.fasta
[2023-06-27 23:46:11,605] [INFO] Task started: Blastn
[2023-06-27 23:46:11,606] [INFO] Running command: blastn -query GCA_002167765.1_ASM216776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/reference_markers.fasta -out GCA_002167765.1_ASM216776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:46:12,257] [INFO] Task succeeded: Blastn
[2023-06-27 23:46:12,261] [INFO] Selected 27 target genomes.
[2023-06-27 23:46:12,262] [INFO] Target genome list was writen to GCA_002167765.1_ASM216776v1_genomic.fna/target_genomes.txt
[2023-06-27 23:46:12,263] [INFO] Task started: fastANI
[2023-06-27 23:46:12,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg69de40bd-bcba-4cf8-81cc-6b1d05024782/GCA_002167765.1_ASM216776v1_genomic.fna.gz --refList GCA_002167765.1_ASM216776v1_genomic.fna/target_genomes.txt --output GCA_002167765.1_ASM216776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 23:46:27,686] [INFO] Task succeeded: fastANI
[2023-06-27 23:46:27,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 23:46:27,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 23:46:27,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 23:46:27,688] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 23:46:27,688] [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
--------------------------------------------------------------------------------
[2023-06-27 23:46:27,690] [INFO] DFAST Taxonomy check result was written to GCA_002167765.1_ASM216776v1_genomic.fna/tc_result.tsv
[2023-06-27 23:46:27,691] [INFO] ===== Taxonomy check completed =====
[2023-06-27 23:46:27,691] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 23:46:27,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/checkm_data
[2023-06-27 23:46:27,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 23:46:27,717] [INFO] Task started: CheckM
[2023-06-27 23:46:27,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002167765.1_ASM216776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002167765.1_ASM216776v1_genomic.fna/checkm_input GCA_002167765.1_ASM216776v1_genomic.fna/checkm_result
[2023-06-27 23:46:50,973] [INFO] Task succeeded: CheckM
[2023-06-27 23:46:50,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 23:46:50,992] [INFO] ===== Completeness check finished =====
[2023-06-27 23:46:50,993] [INFO] ===== Start GTDB Search =====
[2023-06-27 23:46:50,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002167765.1_ASM216776v1_genomic.fna/markers.fasta)
[2023-06-27 23:46:50,993] [INFO] Task started: Blastn
[2023-06-27 23:46:50,993] [INFO] Running command: blastn -query GCA_002167765.1_ASM216776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcceb946-70f6-458a-b6a5-836c018f8f01/dqc_reference/reference_markers_gtdb.fasta -out GCA_002167765.1_ASM216776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:46:52,032] [INFO] Task succeeded: Blastn
[2023-06-27 23:46:52,036] [INFO] Selected 23 target genomes.
[2023-06-27 23:46:52,036] [INFO] Target genome list was writen to GCA_002167765.1_ASM216776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 23:46:52,042] [INFO] Task started: fastANI
[2023-06-27 23:46:52,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg69de40bd-bcba-4cf8-81cc-6b1d05024782/GCA_002167765.1_ASM216776v1_genomic.fna.gz --refList GCA_002167765.1_ASM216776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002167765.1_ASM216776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 23:47:02,854] [INFO] Task succeeded: fastANI
[2023-06-27 23:47:02,861] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 23:47:02,861] [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_002456975.1	s__Luminiphilus sp002456975	99.5876	550	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.72	99.71	0.90	0.87	3	conclusive
GCA_002862405.1	s__Luminiphilus sp002862405	78.1101	68	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_902547755.1	s__Luminiphilus sp902547755	77.8078	61	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.4754	71	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.273	86	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	76.5971	52	759	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-27 23:47:02,863] [INFO] GTDB search result was written to GCA_002167765.1_ASM216776v1_genomic.fna/result_gtdb.tsv
[2023-06-27 23:47:02,864] [INFO] ===== GTDB Search completed =====
[2023-06-27 23:47:02,867] [INFO] DFAST_QC result json was written to GCA_002167765.1_ASM216776v1_genomic.fna/dqc_result.json
[2023-06-27 23:47:02,867] [INFO] DFAST_QC completed!
[2023-06-27 23:47:02,867] [INFO] Total running time: 0h0m59s