[2023-06-19 10:56:04,111] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:04,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:04,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference
[2023-06-19 10:56:05,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:05,648] [INFO] Task started: Prodigal
[2023-06-19 10:56:05,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg2be188ad-3ad1-48a9-b924-5fb1ce5af2f0/GCA_018002595.1_ASM1800259v1_genomic.fna.gz | prodigal -d GCA_018002595.1_ASM1800259v1_genomic.fna/cds.fna -a GCA_018002595.1_ASM1800259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:07,196] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:07,196] [INFO] Task started: HMMsearch
[2023-06-19 10:56:07,197] [INFO] Running command: hmmsearch --tblout GCA_018002595.1_ASM1800259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/reference_markers.hmm GCA_018002595.1_ASM1800259v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:07,373] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:07,375] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2be188ad-3ad1-48a9-b924-5fb1ce5af2f0/GCA_018002595.1_ASM1800259v1_genomic.fna.gz]
[2023-06-19 10:56:07,405] [INFO] Query marker FASTA was written to GCA_018002595.1_ASM1800259v1_genomic.fna/markers.fasta
[2023-06-19 10:56:07,405] [INFO] Task started: Blastn
[2023-06-19 10:56:07,405] [INFO] Running command: blastn -query GCA_018002595.1_ASM1800259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/reference_markers.fasta -out GCA_018002595.1_ASM1800259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:09,007] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:09,013] [INFO] Selected 15 target genomes.
[2023-06-19 10:56:09,014] [INFO] Target genome list was writen to GCA_018002595.1_ASM1800259v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:09,022] [INFO] Task started: fastANI
[2023-06-19 10:56:09,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be188ad-3ad1-48a9-b924-5fb1ce5af2f0/GCA_018002595.1_ASM1800259v1_genomic.fna.gz --refList GCA_018002595.1_ASM1800259v1_genomic.fna/target_genomes.txt --output GCA_018002595.1_ASM1800259v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:16,577] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:16,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:16,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:16,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:16,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:56:16,582] [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 10:56:16,592] [INFO] DFAST Taxonomy check result was written to GCA_018002595.1_ASM1800259v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:16,593] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:16,594] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:16,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/checkm_data
[2023-06-19 10:56:16,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:16,615] [INFO] Task started: CheckM
[2023-06-19 10:56:16,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018002595.1_ASM1800259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018002595.1_ASM1800259v1_genomic.fna/checkm_input GCA_018002595.1_ASM1800259v1_genomic.fna/checkm_result
[2023-06-19 10:56:30,401] [INFO] Task succeeded: CheckM
[2023-06-19 10:56:30,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:56:30,426] [INFO] ===== Completeness check finished =====
[2023-06-19 10:56:30,426] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:56:30,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018002595.1_ASM1800259v1_genomic.fna/markers.fasta)
[2023-06-19 10:56:30,427] [INFO] Task started: Blastn
[2023-06-19 10:56:30,427] [INFO] Running command: blastn -query GCA_018002595.1_ASM1800259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bd7f384-4266-422d-9ade-7e9d49f015fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_018002595.1_ASM1800259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:31,109] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:31,113] [INFO] Selected 11 target genomes.
[2023-06-19 10:56:31,114] [INFO] Target genome list was writen to GCA_018002595.1_ASM1800259v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:56:31,122] [INFO] Task started: fastANI
[2023-06-19 10:56:31,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be188ad-3ad1-48a9-b924-5fb1ce5af2f0/GCA_018002595.1_ASM1800259v1_genomic.fna.gz --refList GCA_018002595.1_ASM1800259v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018002595.1_ASM1800259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:56:35,682] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:35,687] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 10:56:35,687] [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_002281095.1	s__GCA-002282575 sp002281095	84.4816	124	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__GCA-002282575	95.0	98.77	98.71	0.84	0.81	6	-
GCA_014763665.1	s__GCA-002282575 sp014763665	84.1887	127	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiomicrospirales;f__Thiomicrospiraceae;g__GCA-002282575	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:56:35,689] [INFO] GTDB search result was written to GCA_018002595.1_ASM1800259v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:56:35,690] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:56:35,693] [INFO] DFAST_QC result json was written to GCA_018002595.1_ASM1800259v1_genomic.fna/dqc_result.json
[2023-06-19 10:56:35,693] [INFO] DFAST_QC completed!
[2023-06-19 10:56:35,693] [INFO] Total running time: 0h0m32s