[2023-06-18 17:26:10,877] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:26:10,881] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:26:10,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference
[2023-06-18 17:26:12,126] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:26:12,127] [INFO] Task started: Prodigal
[2023-06-18 17:26:12,127] [INFO] Running command: gunzip -c /var/lib/cwl/stga4dda111-d1d9-465f-b087-50f4b075cf6e/GCA_018064855.1_ASM1806485v1_genomic.fna.gz | prodigal -d GCA_018064855.1_ASM1806485v1_genomic.fna/cds.fna -a GCA_018064855.1_ASM1806485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:26:28,945] [INFO] Task succeeded: Prodigal
[2023-06-18 17:26:28,946] [INFO] Task started: HMMsearch
[2023-06-18 17:26:28,946] [INFO] Running command: hmmsearch --tblout GCA_018064855.1_ASM1806485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/reference_markers.hmm GCA_018064855.1_ASM1806485v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:26:29,206] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:26:29,207] [INFO] Found 6/6 markers.
[2023-06-18 17:26:29,238] [INFO] Query marker FASTA was written to GCA_018064855.1_ASM1806485v1_genomic.fna/markers.fasta
[2023-06-18 17:26:29,239] [INFO] Task started: Blastn
[2023-06-18 17:26:29,239] [INFO] Running command: blastn -query GCA_018064855.1_ASM1806485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/reference_markers.fasta -out GCA_018064855.1_ASM1806485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:26:29,814] [INFO] Task succeeded: Blastn
[2023-06-18 17:26:29,821] [INFO] Selected 26 target genomes.
[2023-06-18 17:26:29,822] [INFO] Target genome list was writen to GCA_018064855.1_ASM1806485v1_genomic.fna/target_genomes.txt
[2023-06-18 17:26:29,828] [INFO] Task started: fastANI
[2023-06-18 17:26:29,828] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dda111-d1d9-465f-b087-50f4b075cf6e/GCA_018064855.1_ASM1806485v1_genomic.fna.gz --refList GCA_018064855.1_ASM1806485v1_genomic.fna/target_genomes.txt --output GCA_018064855.1_ASM1806485v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:26:45,136] [INFO] Task succeeded: fastANI
[2023-06-18 17:26:45,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:26:45,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:26:45,140] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:26:45,140] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:26:45,140] [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 17:26:45,143] [INFO] DFAST Taxonomy check result was written to GCA_018064855.1_ASM1806485v1_genomic.fna/tc_result.tsv
[2023-06-18 17:26:45,144] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:26:45,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:26:45,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/checkm_data
[2023-06-18 17:26:45,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:26:45,183] [INFO] Task started: CheckM
[2023-06-18 17:26:45,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064855.1_ASM1806485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064855.1_ASM1806485v1_genomic.fna/checkm_input GCA_018064855.1_ASM1806485v1_genomic.fna/checkm_result
[2023-06-18 17:27:37,382] [INFO] Task succeeded: CheckM
[2023-06-18 17:27:37,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:27:37,418] [INFO] ===== Completeness check finished =====
[2023-06-18 17:27:37,418] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:27:37,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064855.1_ASM1806485v1_genomic.fna/markers.fasta)
[2023-06-18 17:27:37,419] [INFO] Task started: Blastn
[2023-06-18 17:27:37,419] [INFO] Running command: blastn -query GCA_018064855.1_ASM1806485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5ffb95-3b8d-46e3-a386-3baf02ccafb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064855.1_ASM1806485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:27:38,230] [INFO] Task succeeded: Blastn
[2023-06-18 17:27:38,236] [INFO] Selected 26 target genomes.
[2023-06-18 17:27:38,236] [INFO] Target genome list was writen to GCA_018064855.1_ASM1806485v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:27:38,275] [INFO] Task started: fastANI
[2023-06-18 17:27:38,275] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dda111-d1d9-465f-b087-50f4b075cf6e/GCA_018064855.1_ASM1806485v1_genomic.fna.gz --refList GCA_018064855.1_ASM1806485v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064855.1_ASM1806485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:27:50,160] [INFO] Task succeeded: fastANI
[2023-06-18 17:27:50,168] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:27:50,168] [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_018064855.1	s__UBA4345 sp018064855	100.0	924	933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA4345	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002362105.1	s__UBA4345 sp002362105	77.613	126	933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA4345	95.0	99.14	98.50	0.91	0.87	6	-
GCA_002396385.1	s__UBA4345 sp002396385	77.448	103	933	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__UBA4345	95.0	97.65	97.12	0.80	0.75	4	-
--------------------------------------------------------------------------------
[2023-06-18 17:27:50,172] [INFO] GTDB search result was written to GCA_018064855.1_ASM1806485v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:27:50,173] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:27:50,175] [INFO] DFAST_QC result json was written to GCA_018064855.1_ASM1806485v1_genomic.fna/dqc_result.json
[2023-06-18 17:27:50,175] [INFO] DFAST_QC completed!
[2023-06-18 17:27:50,175] [INFO] Total running time: 0h1m39s