[2023-06-13 23:45:32,550] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:45:32,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:45:32,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference
[2023-06-13 23:45:33,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:45:33,700] [INFO] Task started: Prodigal
[2023-06-13 23:45:33,700] [INFO] Running command: gunzip -c /var/lib/cwl/stge4e954af-57e4-4204-ae97-2be2c79dec26/GCA_022560735.1_ASM2256073v1_genomic.fna.gz | prodigal -d GCA_022560735.1_ASM2256073v1_genomic.fna/cds.fna -a GCA_022560735.1_ASM2256073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:45:40,922] [INFO] Task succeeded: Prodigal
[2023-06-13 23:45:40,923] [INFO] Task started: HMMsearch
[2023-06-13 23:45:40,923] [INFO] Running command: hmmsearch --tblout GCA_022560735.1_ASM2256073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/reference_markers.hmm GCA_022560735.1_ASM2256073v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:45:41,162] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:45:41,163] [INFO] Found 6/6 markers.
[2023-06-13 23:45:41,190] [INFO] Query marker FASTA was written to GCA_022560735.1_ASM2256073v1_genomic.fna/markers.fasta
[2023-06-13 23:45:41,191] [INFO] Task started: Blastn
[2023-06-13 23:45:41,191] [INFO] Running command: blastn -query GCA_022560735.1_ASM2256073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/reference_markers.fasta -out GCA_022560735.1_ASM2256073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:45:41,861] [INFO] Task succeeded: Blastn
[2023-06-13 23:45:41,864] [INFO] Selected 35 target genomes.
[2023-06-13 23:45:41,865] [INFO] Target genome list was writen to GCA_022560735.1_ASM2256073v1_genomic.fna/target_genomes.txt
[2023-06-13 23:45:41,866] [INFO] Task started: fastANI
[2023-06-13 23:45:41,866] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e954af-57e4-4204-ae97-2be2c79dec26/GCA_022560735.1_ASM2256073v1_genomic.fna.gz --refList GCA_022560735.1_ASM2256073v1_genomic.fna/target_genomes.txt --output GCA_022560735.1_ASM2256073v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:46:06,144] [INFO] Task succeeded: fastANI
[2023-06-13 23:46:06,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:46:06,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:46:06,147] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:46:06,147] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 23:46:06,147] [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
--------------------------------------------------------------------------------
[2023-06-13 23:46:06,149] [INFO] DFAST Taxonomy check result was written to GCA_022560735.1_ASM2256073v1_genomic.fna/tc_result.tsv
[2023-06-13 23:46:06,149] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:46:06,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:46:06,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/checkm_data
[2023-06-13 23:46:06,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:46:06,181] [INFO] Task started: CheckM
[2023-06-13 23:46:06,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022560735.1_ASM2256073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022560735.1_ASM2256073v1_genomic.fna/checkm_input GCA_022560735.1_ASM2256073v1_genomic.fna/checkm_result
[2023-06-13 23:46:30,437] [INFO] Task succeeded: CheckM
[2023-06-13 23:46:30,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:46:30,455] [INFO] ===== Completeness check finished =====
[2023-06-13 23:46:30,456] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:46:30,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022560735.1_ASM2256073v1_genomic.fna/markers.fasta)
[2023-06-13 23:46:30,456] [INFO] Task started: Blastn
[2023-06-13 23:46:30,457] [INFO] Running command: blastn -query GCA_022560735.1_ASM2256073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33637228-c7fe-4a6a-a755-cca6d9020f69/dqc_reference/reference_markers_gtdb.fasta -out GCA_022560735.1_ASM2256073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:46:31,628] [INFO] Task succeeded: Blastn
[2023-06-13 23:46:31,636] [INFO] Selected 31 target genomes.
[2023-06-13 23:46:31,636] [INFO] Target genome list was writen to GCA_022560735.1_ASM2256073v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:46:31,644] [INFO] Task started: fastANI
[2023-06-13 23:46:31,644] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e954af-57e4-4204-ae97-2be2c79dec26/GCA_022560735.1_ASM2256073v1_genomic.fna.gz --refList GCA_022560735.1_ASM2256073v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022560735.1_ASM2256073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:46:48,380] [INFO] Task succeeded: fastANI
[2023-06-13 23:46:48,384] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:46:48,384] [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_008975185.1	s__MnTg04 sp008975185	88.5288	414	889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__MnTg04;f__MnTg04;g__MnTg04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695765.1	s__J054 sp003695765	75.9135	66	889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__J054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	75.764	51	889	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-13 23:46:48,386] [INFO] GTDB search result was written to GCA_022560735.1_ASM2256073v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:46:48,386] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:46:48,388] [INFO] DFAST_QC result json was written to GCA_022560735.1_ASM2256073v1_genomic.fna/dqc_result.json
[2023-06-13 23:46:48,388] [INFO] DFAST_QC completed!
[2023-06-13 23:46:48,388] [INFO] Total running time: 0h1m16s