[2023-06-13 20:43:23,379] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:43:23,381] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:43:23,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference
[2023-06-13 20:43:26,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:43:26,383] [INFO] Task started: Prodigal
[2023-06-13 20:43:26,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgac005dba-0047-42ad-bf4d-6d91392d7b5b/GCA_022825385.1_ASM2282538v1_genomic.fna.gz | prodigal -d GCA_022825385.1_ASM2282538v1_genomic.fna/cds.fna -a GCA_022825385.1_ASM2282538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:43:44,096] [INFO] Task succeeded: Prodigal
[2023-06-13 20:43:44,097] [INFO] Task started: HMMsearch
[2023-06-13 20:43:44,097] [INFO] Running command: hmmsearch --tblout GCA_022825385.1_ASM2282538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/reference_markers.hmm GCA_022825385.1_ASM2282538v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:43:44,305] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:43:44,307] [INFO] Found 6/6 markers.
[2023-06-13 20:43:44,333] [INFO] Query marker FASTA was written to GCA_022825385.1_ASM2282538v1_genomic.fna/markers.fasta
[2023-06-13 20:43:44,334] [INFO] Task started: Blastn
[2023-06-13 20:43:44,334] [INFO] Running command: blastn -query GCA_022825385.1_ASM2282538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/reference_markers.fasta -out GCA_022825385.1_ASM2282538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:43:45,009] [INFO] Task succeeded: Blastn
[2023-06-13 20:43:45,013] [INFO] Selected 32 target genomes.
[2023-06-13 20:43:45,014] [INFO] Target genome list was writen to GCA_022825385.1_ASM2282538v1_genomic.fna/target_genomes.txt
[2023-06-13 20:43:45,017] [INFO] Task started: fastANI
[2023-06-13 20:43:45,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgac005dba-0047-42ad-bf4d-6d91392d7b5b/GCA_022825385.1_ASM2282538v1_genomic.fna.gz --refList GCA_022825385.1_ASM2282538v1_genomic.fna/target_genomes.txt --output GCA_022825385.1_ASM2282538v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:44:08,877] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:08,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:44:08,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:44:08,882] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:44:08,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:44:08,882] [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
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.1919	65	982	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:44:08,884] [INFO] DFAST Taxonomy check result was written to GCA_022825385.1_ASM2282538v1_genomic.fna/tc_result.tsv
[2023-06-13 20:44:08,884] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:44:08,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:44:08,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/checkm_data
[2023-06-13 20:44:08,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:44:08,914] [INFO] Task started: CheckM
[2023-06-13 20:44:08,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022825385.1_ASM2282538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022825385.1_ASM2282538v1_genomic.fna/checkm_input GCA_022825385.1_ASM2282538v1_genomic.fna/checkm_result
[2023-06-13 20:44:55,947] [INFO] Task succeeded: CheckM
[2023-06-13 20:44:55,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:44:55,966] [INFO] ===== Completeness check finished =====
[2023-06-13 20:44:55,966] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:44:55,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022825385.1_ASM2282538v1_genomic.fna/markers.fasta)
[2023-06-13 20:44:55,967] [INFO] Task started: Blastn
[2023-06-13 20:44:55,967] [INFO] Running command: blastn -query GCA_022825385.1_ASM2282538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16352623-cc65-485b-bee2-57978c90d64d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022825385.1_ASM2282538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:57,052] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:57,057] [INFO] Selected 29 target genomes.
[2023-06-13 20:44:57,057] [INFO] Target genome list was writen to GCA_022825385.1_ASM2282538v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:44:57,067] [INFO] Task started: fastANI
[2023-06-13 20:44:57,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgac005dba-0047-42ad-bf4d-6d91392d7b5b/GCA_022825385.1_ASM2282538v1_genomic.fna.gz --refList GCA_022825385.1_ASM2282538v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022825385.1_ASM2282538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:45:12,379] [INFO] Task succeeded: fastANI
[2023-06-13 20:45:12,384] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 20:45:12,384] [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_009839485.1	s__VXPQ01 sp009839485	80.541	576	982	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__VXPQ01;g__VXPQ01	95.0	99.91	99.91	0.98	0.98	2	-
GCA_003285105.1	s__MEBICO9517 sp003285105	76.2678	65	982	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCA_011682235.1	s__ISCAR-4553 sp011682235	76.2209	62	982	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__ISCAR-4553;g__ISCAR-4553	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:45:12,386] [INFO] GTDB search result was written to GCA_022825385.1_ASM2282538v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:45:12,387] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:45:12,390] [INFO] DFAST_QC result json was written to GCA_022825385.1_ASM2282538v1_genomic.fna/dqc_result.json
[2023-06-13 20:45:12,391] [INFO] DFAST_QC completed!
[2023-06-13 20:45:12,391] [INFO] Total running time: 0h1m49s