[2023-06-19 01:08:26,675] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:08:26,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:08:26,680] [INFO] DQC Reference Directory: /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference
[2023-06-19 01:08:30,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:08:30,268] [INFO] Task started: Prodigal
[2023-06-19 01:08:30,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3a4950a-15f8-417e-a328-0d3e627497df/GCA_018883445.1_ASM1888344v1_genomic.fna.gz | prodigal -d GCA_018883445.1_ASM1888344v1_genomic.fna/cds.fna -a GCA_018883445.1_ASM1888344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:08:33,653] [INFO] Task succeeded: Prodigal
[2023-06-19 01:08:33,654] [INFO] Task started: HMMsearch
[2023-06-19 01:08:33,654] [INFO] Running command: hmmsearch --tblout GCA_018883445.1_ASM1888344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/reference_markers.hmm GCA_018883445.1_ASM1888344v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:08:33,861] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:08:33,862] [INFO] Found 6/6 markers.
[2023-06-19 01:08:33,903] [INFO] Query marker FASTA was written to GCA_018883445.1_ASM1888344v1_genomic.fna/markers.fasta
[2023-06-19 01:08:33,904] [INFO] Task started: Blastn
[2023-06-19 01:08:33,904] [INFO] Running command: blastn -query GCA_018883445.1_ASM1888344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/reference_markers.fasta -out GCA_018883445.1_ASM1888344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:08:36,817] [INFO] Task succeeded: Blastn
[2023-06-19 01:08:36,821] [INFO] Selected 29 target genomes.
[2023-06-19 01:08:36,821] [INFO] Target genome list was writen to GCA_018883445.1_ASM1888344v1_genomic.fna/target_genomes.txt
[2023-06-19 01:08:36,828] [INFO] Task started: fastANI
[2023-06-19 01:08:36,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a4950a-15f8-417e-a328-0d3e627497df/GCA_018883445.1_ASM1888344v1_genomic.fna.gz --refList GCA_018883445.1_ASM1888344v1_genomic.fna/target_genomes.txt --output GCA_018883445.1_ASM1888344v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:08:52,103] [INFO] Task succeeded: fastANI
[2023-06-19 01:08:52,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:08:52,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:08:52,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:08:52,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 01:08:52,106] [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 01:08:52,108] [INFO] DFAST Taxonomy check result was written to GCA_018883445.1_ASM1888344v1_genomic.fna/tc_result.tsv
[2023-06-19 01:08:52,110] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:08:52,111] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:08:52,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/checkm_data
[2023-06-19 01:08:52,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:08:52,137] [INFO] Task started: CheckM
[2023-06-19 01:08:52,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018883445.1_ASM1888344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018883445.1_ASM1888344v1_genomic.fna/checkm_input GCA_018883445.1_ASM1888344v1_genomic.fna/checkm_result
[2023-06-19 01:09:11,275] [INFO] Task succeeded: CheckM
[2023-06-19 01:09:11,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:09:11,306] [INFO] ===== Completeness check finished =====
[2023-06-19 01:09:11,307] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:09:11,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018883445.1_ASM1888344v1_genomic.fna/markers.fasta)
[2023-06-19 01:09:11,308] [INFO] Task started: Blastn
[2023-06-19 01:09:11,308] [INFO] Running command: blastn -query GCA_018883445.1_ASM1888344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47058dc-9f47-442e-90d3-3942d390e803/dqc_reference/reference_markers_gtdb.fasta -out GCA_018883445.1_ASM1888344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:09:12,164] [INFO] Task succeeded: Blastn
[2023-06-19 01:09:12,169] [INFO] Selected 24 target genomes.
[2023-06-19 01:09:12,170] [INFO] Target genome list was writen to GCA_018883445.1_ASM1888344v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:09:12,189] [INFO] Task started: fastANI
[2023-06-19 01:09:12,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a4950a-15f8-417e-a328-0d3e627497df/GCA_018883445.1_ASM1888344v1_genomic.fna.gz --refList GCA_018883445.1_ASM1888344v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018883445.1_ASM1888344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:09:19,839] [INFO] Task succeeded: fastANI
[2023-06-19 01:09:19,849] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:09:19,849] [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_009926205.1	s__RFPI01 sp009926205	98.9692	351	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__RFPI01	95.0	98.97	98.97	0.90	0.90	2	conclusive
GCF_000953015.1	s__Methylopumilus_A turicensis	76.9228	69	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899965.1	s__Methylopumilus_A sp903899965	76.6465	62	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	98.90	98.39	0.92	0.86	12	-
GCA_903870165.1	s__Methylopumilus_A sp903870165	76.5165	60	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.91	99.91	0.89	0.89	2	-
GCA_903870995.1	s__Methylopumilus_A sp903870995	76.3695	70	388	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus_A	95.0	99.94	99.94	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-19 01:09:19,851] [INFO] GTDB search result was written to GCA_018883445.1_ASM1888344v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:09:19,852] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:09:19,855] [INFO] DFAST_QC result json was written to GCA_018883445.1_ASM1888344v1_genomic.fna/dqc_result.json
[2023-06-19 01:09:19,855] [INFO] DFAST_QC completed!
[2023-06-19 01:09:19,856] [INFO] Total running time: 0h0m53s