[2023-06-19 07:50:09,328] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:50:09,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:50:09,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference
[2023-06-19 07:50:10,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:50:10,562] [INFO] Task started: Prodigal
[2023-06-19 07:50:10,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg39c370f2-0a82-46a9-873c-6b5a2ef25e4f/GCA_018701255.1_ASM1870125v1_genomic.fna.gz | prodigal -d GCA_018701255.1_ASM1870125v1_genomic.fna/cds.fna -a GCA_018701255.1_ASM1870125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:50:15,517] [INFO] Task succeeded: Prodigal
[2023-06-19 07:50:15,517] [INFO] Task started: HMMsearch
[2023-06-19 07:50:15,517] [INFO] Running command: hmmsearch --tblout GCA_018701255.1_ASM1870125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/reference_markers.hmm GCA_018701255.1_ASM1870125v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:50:15,765] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:50:15,766] [INFO] Found 6/6 markers.
[2023-06-19 07:50:15,792] [INFO] Query marker FASTA was written to GCA_018701255.1_ASM1870125v1_genomic.fna/markers.fasta
[2023-06-19 07:50:15,793] [INFO] Task started: Blastn
[2023-06-19 07:50:15,793] [INFO] Running command: blastn -query GCA_018701255.1_ASM1870125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/reference_markers.fasta -out GCA_018701255.1_ASM1870125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:16,420] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:16,423] [INFO] Selected 30 target genomes.
[2023-06-19 07:50:16,424] [INFO] Target genome list was writen to GCA_018701255.1_ASM1870125v1_genomic.fna/target_genomes.txt
[2023-06-19 07:50:16,429] [INFO] Task started: fastANI
[2023-06-19 07:50:16,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c370f2-0a82-46a9-873c-6b5a2ef25e4f/GCA_018701255.1_ASM1870125v1_genomic.fna.gz --refList GCA_018701255.1_ASM1870125v1_genomic.fna/target_genomes.txt --output GCA_018701255.1_ASM1870125v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:50:33,251] [INFO] Task succeeded: fastANI
[2023-06-19 07:50:33,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:50:33,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:50:33,258] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:50:33,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 07:50:33,259] [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
--------------------------------------------------------------------------------
[2023-06-19 07:50:33,261] [INFO] DFAST Taxonomy check result was written to GCA_018701255.1_ASM1870125v1_genomic.fna/tc_result.tsv
[2023-06-19 07:50:33,262] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:50:33,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:50:33,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/checkm_data
[2023-06-19 07:50:33,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:50:33,294] [INFO] Task started: CheckM
[2023-06-19 07:50:33,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018701255.1_ASM1870125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018701255.1_ASM1870125v1_genomic.fna/checkm_input GCA_018701255.1_ASM1870125v1_genomic.fna/checkm_result
[2023-06-19 07:50:55,505] [INFO] Task succeeded: CheckM
[2023-06-19 07:50:55,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 07:50:55,535] [INFO] ===== Completeness check finished =====
[2023-06-19 07:50:55,536] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:50:55,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018701255.1_ASM1870125v1_genomic.fna/markers.fasta)
[2023-06-19 07:50:55,536] [INFO] Task started: Blastn
[2023-06-19 07:50:55,537] [INFO] Running command: blastn -query GCA_018701255.1_ASM1870125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34c1b93b-dd0e-4f6b-8d73-99ef82f15069/dqc_reference/reference_markers_gtdb.fasta -out GCA_018701255.1_ASM1870125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:50:56,624] [INFO] Task succeeded: Blastn
[2023-06-19 07:50:56,628] [INFO] Selected 18 target genomes.
[2023-06-19 07:50:56,628] [INFO] Target genome list was writen to GCA_018701255.1_ASM1870125v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:50:56,634] [INFO] Task started: fastANI
[2023-06-19 07:50:56,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg39c370f2-0a82-46a9-873c-6b5a2ef25e4f/GCA_018701255.1_ASM1870125v1_genomic.fna.gz --refList GCA_018701255.1_ASM1870125v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018701255.1_ASM1870125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:51:02,633] [INFO] Task succeeded: fastANI
[2023-06-19 07:51:02,647] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:51:02,647] [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_018701255.1	s__UBA12202 sp018701255	100.0	559	570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016778985.1	s__UBA12202 sp016778985	78.8984	336	570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691725.1	s__UBA12202 sp002691725	78.8677	297	570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__UBA1172;g__UBA12202	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:51:02,650] [INFO] GTDB search result was written to GCA_018701255.1_ASM1870125v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:51:02,651] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:51:02,654] [INFO] DFAST_QC result json was written to GCA_018701255.1_ASM1870125v1_genomic.fna/dqc_result.json
[2023-06-19 07:51:02,654] [INFO] DFAST_QC completed!
[2023-06-19 07:51:02,654] [INFO] Total running time: 0h0m53s