[2023-06-18 20:48:02,747] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:48:02,749] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:48:02,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference
[2023-06-18 20:48:04,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:48:04,972] [INFO] Task started: Prodigal
[2023-06-18 20:48:04,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg647c377d-2add-40a2-8923-40346b01b148/GCA_018659465.1_ASM1865946v1_genomic.fna.gz | prodigal -d GCA_018659465.1_ASM1865946v1_genomic.fna/cds.fna -a GCA_018659465.1_ASM1865946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:48:11,009] [INFO] Task succeeded: Prodigal
[2023-06-18 20:48:11,010] [INFO] Task started: HMMsearch
[2023-06-18 20:48:11,010] [INFO] Running command: hmmsearch --tblout GCA_018659465.1_ASM1865946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/reference_markers.hmm GCA_018659465.1_ASM1865946v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:48:11,255] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:48:11,257] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg647c377d-2add-40a2-8923-40346b01b148/GCA_018659465.1_ASM1865946v1_genomic.fna.gz]
[2023-06-18 20:48:11,285] [INFO] Query marker FASTA was written to GCA_018659465.1_ASM1865946v1_genomic.fna/markers.fasta
[2023-06-18 20:48:11,285] [INFO] Task started: Blastn
[2023-06-18 20:48:11,285] [INFO] Running command: blastn -query GCA_018659465.1_ASM1865946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/reference_markers.fasta -out GCA_018659465.1_ASM1865946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:48:11,893] [INFO] Task succeeded: Blastn
[2023-06-18 20:48:11,897] [INFO] Selected 10 target genomes.
[2023-06-18 20:48:11,898] [INFO] Target genome list was writen to GCA_018659465.1_ASM1865946v1_genomic.fna/target_genomes.txt
[2023-06-18 20:48:11,901] [INFO] Task started: fastANI
[2023-06-18 20:48:11,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg647c377d-2add-40a2-8923-40346b01b148/GCA_018659465.1_ASM1865946v1_genomic.fna.gz --refList GCA_018659465.1_ASM1865946v1_genomic.fna/target_genomes.txt --output GCA_018659465.1_ASM1865946v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:48:18,216] [INFO] Task succeeded: fastANI
[2023-06-18 20:48:18,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:48:18,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:48:18,219] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:48:18,219] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:48:18,219] [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 20:48:18,221] [INFO] DFAST Taxonomy check result was written to GCA_018659465.1_ASM1865946v1_genomic.fna/tc_result.tsv
[2023-06-18 20:48:18,222] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:48:18,222] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:48:18,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/checkm_data
[2023-06-18 20:48:18,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:48:18,255] [INFO] Task started: CheckM
[2023-06-18 20:48:18,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659465.1_ASM1865946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659465.1_ASM1865946v1_genomic.fna/checkm_input GCA_018659465.1_ASM1865946v1_genomic.fna/checkm_result
[2023-06-18 20:48:43,124] [INFO] Task succeeded: CheckM
[2023-06-18 20:48:43,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.84%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-18 20:48:43,146] [INFO] ===== Completeness check finished =====
[2023-06-18 20:48:43,147] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:48:43,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659465.1_ASM1865946v1_genomic.fna/markers.fasta)
[2023-06-18 20:48:43,148] [INFO] Task started: Blastn
[2023-06-18 20:48:43,148] [INFO] Running command: blastn -query GCA_018659465.1_ASM1865946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d839353-72da-4b77-9c3e-eddb49847bc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659465.1_ASM1865946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:48:44,101] [INFO] Task succeeded: Blastn
[2023-06-18 20:48:44,105] [INFO] Selected 7 target genomes.
[2023-06-18 20:48:44,105] [INFO] Target genome list was writen to GCA_018659465.1_ASM1865946v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:48:44,105] [INFO] Task started: fastANI
[2023-06-18 20:48:44,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg647c377d-2add-40a2-8923-40346b01b148/GCA_018659465.1_ASM1865946v1_genomic.fna.gz --refList GCA_018659465.1_ASM1865946v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659465.1_ASM1865946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:48:48,120] [INFO] Task succeeded: fastANI
[2023-06-18 20:48:48,130] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:48:48,130] [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_018694455.1	s__UBA1268 sp018694455	98.8109	498	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	98.58	0.79	0.76	6	conclusive
GCA_014238855.1	s__UBA1268 sp014238855	88.1372	464	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862165.1	s__UBA1268 sp002862165	86.0219	345	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776925.1	s__UBA1268 sp016776925	80.2598	284	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	96.90	0.88	0.85	13	-
GCA_905477565.1	s__UBA1268 sp905477565	80.0492	158	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509235.1	s__UBA1268 sp003509235	79.818	211	590	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:48:48,132] [INFO] GTDB search result was written to GCA_018659465.1_ASM1865946v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:48:48,132] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:48:48,135] [INFO] DFAST_QC result json was written to GCA_018659465.1_ASM1865946v1_genomic.fna/dqc_result.json
[2023-06-18 20:48:48,135] [INFO] DFAST_QC completed!
[2023-06-18 20:48:48,135] [INFO] Total running time: 0h0m45s