[2023-06-19 13:42:56,760] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:42:56,768] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:42:56,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference
[2023-06-19 13:42:58,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:42:58,050] [INFO] Task started: Prodigal
[2023-06-19 13:42:58,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg40ebb730-61c2-41cd-92cc-6a11f9b440ad/GCA_018648845.1_ASM1864884v1_genomic.fna.gz | prodigal -d GCA_018648845.1_ASM1864884v1_genomic.fna/cds.fna -a GCA_018648845.1_ASM1864884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:43:10,394] [INFO] Task succeeded: Prodigal
[2023-06-19 13:43:10,394] [INFO] Task started: HMMsearch
[2023-06-19 13:43:10,394] [INFO] Running command: hmmsearch --tblout GCA_018648845.1_ASM1864884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/reference_markers.hmm GCA_018648845.1_ASM1864884v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:43:10,677] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:43:10,678] [INFO] Found 6/6 markers.
[2023-06-19 13:43:10,711] [INFO] Query marker FASTA was written to GCA_018648845.1_ASM1864884v1_genomic.fna/markers.fasta
[2023-06-19 13:43:10,711] [INFO] Task started: Blastn
[2023-06-19 13:43:10,711] [INFO] Running command: blastn -query GCA_018648845.1_ASM1864884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/reference_markers.fasta -out GCA_018648845.1_ASM1864884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:11,305] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:11,309] [INFO] Selected 32 target genomes.
[2023-06-19 13:43:11,310] [INFO] Target genome list was writen to GCA_018648845.1_ASM1864884v1_genomic.fna/target_genomes.txt
[2023-06-19 13:43:11,315] [INFO] Task started: fastANI
[2023-06-19 13:43:11,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ebb730-61c2-41cd-92cc-6a11f9b440ad/GCA_018648845.1_ASM1864884v1_genomic.fna.gz --refList GCA_018648845.1_ASM1864884v1_genomic.fna/target_genomes.txt --output GCA_018648845.1_ASM1864884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:43:29,474] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:29,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:43:29,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:43:29,477] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:43:29,477] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:43:29,477] [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 13:43:29,479] [INFO] DFAST Taxonomy check result was written to GCA_018648845.1_ASM1864884v1_genomic.fna/tc_result.tsv
[2023-06-19 13:43:29,480] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:43:29,480] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:43:29,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/checkm_data
[2023-06-19 13:43:29,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:43:29,524] [INFO] Task started: CheckM
[2023-06-19 13:43:29,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018648845.1_ASM1864884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018648845.1_ASM1864884v1_genomic.fna/checkm_input GCA_018648845.1_ASM1864884v1_genomic.fna/checkm_result
[2023-06-19 13:44:09,434] [INFO] Task succeeded: CheckM
[2023-06-19 13:44:09,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:44:09,459] [INFO] ===== Completeness check finished =====
[2023-06-19 13:44:09,459] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:44:09,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018648845.1_ASM1864884v1_genomic.fna/markers.fasta)
[2023-06-19 13:44:09,460] [INFO] Task started: Blastn
[2023-06-19 13:44:09,460] [INFO] Running command: blastn -query GCA_018648845.1_ASM1864884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c81cca-112b-4118-8688-21d8616b0fc6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018648845.1_ASM1864884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:44:10,196] [INFO] Task succeeded: Blastn
[2023-06-19 13:44:10,201] [INFO] Selected 29 target genomes.
[2023-06-19 13:44:10,202] [INFO] Target genome list was writen to GCA_018648845.1_ASM1864884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:44:10,214] [INFO] Task started: fastANI
[2023-06-19 13:44:10,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg40ebb730-61c2-41cd-92cc-6a11f9b440ad/GCA_018648845.1_ASM1864884v1_genomic.fna.gz --refList GCA_018648845.1_ASM1864884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018648845.1_ASM1864884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:44:26,239] [INFO] Task succeeded: fastANI
[2023-06-19 13:44:26,244] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:44:26,244] [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_018698135.1	s__JABINZ01 sp018698135	99.6194	906	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__CAILMK01;f__JAAYUY01;g__JABINZ01	95.0	99.42	99.36	0.86	0.82	13	conclusive
--------------------------------------------------------------------------------
[2023-06-19 13:44:26,247] [INFO] GTDB search result was written to GCA_018648845.1_ASM1864884v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:44:26,247] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:44:26,250] [INFO] DFAST_QC result json was written to GCA_018648845.1_ASM1864884v1_genomic.fna/dqc_result.json
[2023-06-19 13:44:26,250] [INFO] DFAST_QC completed!
[2023-06-19 13:44:26,250] [INFO] Total running time: 0h1m29s