[2023-06-18 13:03:42,054] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:42,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:42,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference
[2023-06-18 13:03:43,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:43,274] [INFO] Task started: Prodigal
[2023-06-18 13:03:43,275] [INFO] Running command: gunzip -c /var/lib/cwl/stga0b91bdd-b8fe-49bc-9039-643406f5eae4/GCA_018607785.1_ASM1860778v1_genomic.fna.gz | prodigal -d GCA_018607785.1_ASM1860778v1_genomic.fna/cds.fna -a GCA_018607785.1_ASM1860778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:45,202] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:45,203] [INFO] Task started: HMMsearch
[2023-06-18 13:03:45,203] [INFO] Running command: hmmsearch --tblout GCA_018607785.1_ASM1860778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/reference_markers.hmm GCA_018607785.1_ASM1860778v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:45,398] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:45,400] [INFO] Found 6/6 markers.
[2023-06-18 13:03:45,425] [INFO] Query marker FASTA was written to GCA_018607785.1_ASM1860778v1_genomic.fna/markers.fasta
[2023-06-18 13:03:45,425] [INFO] Task started: Blastn
[2023-06-18 13:03:45,425] [INFO] Running command: blastn -query GCA_018607785.1_ASM1860778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/reference_markers.fasta -out GCA_018607785.1_ASM1860778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:46,500] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:46,505] [INFO] Selected 21 target genomes.
[2023-06-18 13:03:46,506] [INFO] Target genome list was writen to GCA_018607785.1_ASM1860778v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:46,524] [INFO] Task started: fastANI
[2023-06-18 13:03:46,525] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b91bdd-b8fe-49bc-9039-643406f5eae4/GCA_018607785.1_ASM1860778v1_genomic.fna.gz --refList GCA_018607785.1_ASM1860778v1_genomic.fna/target_genomes.txt --output GCA_018607785.1_ASM1860778v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:03:54,605] [INFO] Task succeeded: fastANI
[2023-06-18 13:03:54,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:03:54,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:03:54,607] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:03:54,607] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:03:54,607] [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 13:03:54,609] [INFO] DFAST Taxonomy check result was written to GCA_018607785.1_ASM1860778v1_genomic.fna/tc_result.tsv
[2023-06-18 13:03:54,612] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:03:54,612] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:03:54,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/checkm_data
[2023-06-18 13:03:54,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:03:54,655] [INFO] Task started: CheckM
[2023-06-18 13:03:54,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607785.1_ASM1860778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607785.1_ASM1860778v1_genomic.fna/checkm_input GCA_018607785.1_ASM1860778v1_genomic.fna/checkm_result
[2023-06-18 13:04:08,188] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:08,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:08,221] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:08,221] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:08,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607785.1_ASM1860778v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:08,222] [INFO] Task started: Blastn
[2023-06-18 13:04:08,222] [INFO] Running command: blastn -query GCA_018607785.1_ASM1860778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841f158-d07b-45d3-b2ef-306c14fada92/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607785.1_ASM1860778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:09,017] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:09,020] [INFO] Selected 19 target genomes.
[2023-06-18 13:04:09,021] [INFO] Target genome list was writen to GCA_018607785.1_ASM1860778v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:09,030] [INFO] Task started: fastANI
[2023-06-18 13:04:09,030] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b91bdd-b8fe-49bc-9039-643406f5eae4/GCA_018607785.1_ASM1860778v1_genomic.fna.gz --refList GCA_018607785.1_ASM1860778v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607785.1_ASM1860778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:15,400] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:15,408] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:15,408] [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_018607785.1	s__BACL14 sp018607785	100.0	351	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.17	98.94	0.86	0.81	5	conclusive
GCA_018657165.1	s__BACL14 sp018657165	80.2766	184	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.24	99.09	0.82	0.76	15	-
GCA_905181685.1	s__BACL14 sp905181685	80.0773	178	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:15,412] [INFO] GTDB search result was written to GCA_018607785.1_ASM1860778v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:15,413] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:15,415] [INFO] DFAST_QC result json was written to GCA_018607785.1_ASM1860778v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:15,415] [INFO] DFAST_QC completed!
[2023-06-18 13:04:15,415] [INFO] Total running time: 0h0m33s