[2023-06-18 14:43:26,060] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:43:26,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:43:26,067] [INFO] DQC Reference Directory: /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference
[2023-06-18 14:43:27,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:43:27,805] [INFO] Task started: Prodigal
[2023-06-18 14:43:27,806] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6fed52a-fff5-4ca7-8bad-847198ea7704/GCA_018659155.1_ASM1865915v1_genomic.fna.gz | prodigal -d GCA_018659155.1_ASM1865915v1_genomic.fna/cds.fna -a GCA_018659155.1_ASM1865915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:43:29,597] [INFO] Task succeeded: Prodigal
[2023-06-18 14:43:29,598] [INFO] Task started: HMMsearch
[2023-06-18 14:43:29,598] [INFO] Running command: hmmsearch --tblout GCA_018659155.1_ASM1865915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/reference_markers.hmm GCA_018659155.1_ASM1865915v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:43:29,882] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:43:29,883] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb6fed52a-fff5-4ca7-8bad-847198ea7704/GCA_018659155.1_ASM1865915v1_genomic.fna.gz]
[2023-06-18 14:43:29,899] [INFO] Query marker FASTA was written to GCA_018659155.1_ASM1865915v1_genomic.fna/markers.fasta
[2023-06-18 14:43:29,900] [INFO] Task started: Blastn
[2023-06-18 14:43:29,900] [INFO] Running command: blastn -query GCA_018659155.1_ASM1865915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/reference_markers.fasta -out GCA_018659155.1_ASM1865915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:43:31,562] [INFO] Task succeeded: Blastn
[2023-06-18 14:43:31,571] [INFO] Selected 24 target genomes.
[2023-06-18 14:43:31,571] [INFO] Target genome list was writen to GCA_018659155.1_ASM1865915v1_genomic.fna/target_genomes.txt
[2023-06-18 14:43:31,578] [INFO] Task started: fastANI
[2023-06-18 14:43:31,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6fed52a-fff5-4ca7-8bad-847198ea7704/GCA_018659155.1_ASM1865915v1_genomic.fna.gz --refList GCA_018659155.1_ASM1865915v1_genomic.fna/target_genomes.txt --output GCA_018659155.1_ASM1865915v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:43:45,264] [INFO] Task succeeded: fastANI
[2023-06-18 14:43:45,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:43:45,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:43:45,266] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:43:45,266] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 14:43:45,266] [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
--------------------------------------------------------------------------------
[2023-06-18 14:43:45,267] [INFO] DFAST Taxonomy check result was written to GCA_018659155.1_ASM1865915v1_genomic.fna/tc_result.tsv
[2023-06-18 14:43:45,270] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:43:45,270] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:43:45,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/checkm_data
[2023-06-18 14:43:45,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:43:45,289] [INFO] Task started: CheckM
[2023-06-18 14:43:45,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659155.1_ASM1865915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659155.1_ASM1865915v1_genomic.fna/checkm_input GCA_018659155.1_ASM1865915v1_genomic.fna/checkm_result
[2023-06-18 14:43:57,715] [INFO] Task succeeded: CheckM
[2023-06-18 14:43:57,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 14:43:57,742] [INFO] ===== Completeness check finished =====
[2023-06-18 14:43:57,742] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:43:57,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659155.1_ASM1865915v1_genomic.fna/markers.fasta)
[2023-06-18 14:43:57,743] [INFO] Task started: Blastn
[2023-06-18 14:43:57,743] [INFO] Running command: blastn -query GCA_018659155.1_ASM1865915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27222127-910a-4686-b8a8-d69b683b3e4c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659155.1_ASM1865915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:43:58,434] [INFO] Task succeeded: Blastn
[2023-06-18 14:43:58,437] [INFO] Selected 19 target genomes.
[2023-06-18 14:43:58,437] [INFO] Target genome list was writen to GCA_018659155.1_ASM1865915v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:43:58,448] [INFO] Task started: fastANI
[2023-06-18 14:43:58,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6fed52a-fff5-4ca7-8bad-847198ea7704/GCA_018659155.1_ASM1865915v1_genomic.fna.gz --refList GCA_018659155.1_ASM1865915v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659155.1_ASM1865915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:44:05,993] [INFO] Task succeeded: fastANI
[2023-06-18 14:44:05,997] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:44:05,997] [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_018607525.1	s__HTCC2207 sp018607525	95.9973	233	256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.00	96.00	0.91	0.91	2	conclusive
GCA_002469845.1	s__HTCC2207 sp002469845	78.5671	91	256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.61	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-18 14:44:06,000] [INFO] GTDB search result was written to GCA_018659155.1_ASM1865915v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:44:06,002] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:44:06,004] [INFO] DFAST_QC result json was written to GCA_018659155.1_ASM1865915v1_genomic.fna/dqc_result.json
[2023-06-18 14:44:06,004] [INFO] DFAST_QC completed!
[2023-06-18 14:44:06,004] [INFO] Total running time: 0h0m40s