[2023-06-04 21:24:56,222] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:24:56,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:24:56,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference
[2023-06-04 21:24:58,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:24:58,895] [INFO] Task started: Prodigal
[2023-06-04 21:24:58,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgab4a0237-76b5-43ec-84c4-69378ee52b99/GCA_004356175.1_ASM435617v1_genomic.fna.gz | prodigal -d GCA_004356175.1_ASM435617v1_genomic.fna/cds.fna -a GCA_004356175.1_ASM435617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:01,770] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:01,771] [INFO] Task started: HMMsearch
[2023-06-04 21:25:01,772] [INFO] Running command: hmmsearch --tblout GCA_004356175.1_ASM435617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/reference_markers.hmm GCA_004356175.1_ASM435617v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:01,954] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:01,956] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgab4a0237-76b5-43ec-84c4-69378ee52b99/GCA_004356175.1_ASM435617v1_genomic.fna.gz]
[2023-06-04 21:25:01,977] [INFO] Query marker FASTA was written to GCA_004356175.1_ASM435617v1_genomic.fna/markers.fasta
[2023-06-04 21:25:01,977] [INFO] Task started: Blastn
[2023-06-04 21:25:01,977] [INFO] Running command: blastn -query GCA_004356175.1_ASM435617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/reference_markers.fasta -out GCA_004356175.1_ASM435617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:03,810] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:03,815] [INFO] Selected 5 target genomes.
[2023-06-04 21:25:03,816] [INFO] Target genome list was writen to GCA_004356175.1_ASM435617v1_genomic.fna/target_genomes.txt
[2023-06-04 21:25:03,873] [INFO] Task started: fastANI
[2023-06-04 21:25:03,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4a0237-76b5-43ec-84c4-69378ee52b99/GCA_004356175.1_ASM435617v1_genomic.fna.gz --refList GCA_004356175.1_ASM435617v1_genomic.fna/target_genomes.txt --output GCA_004356175.1_ASM435617v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:25:09,515] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:09,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:25:09,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:25:09,518] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:25:09,518] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:25:09,519] [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
--------------------------------------------------------------------------------
[2023-06-04 21:25:09,521] [INFO] DFAST Taxonomy check result was written to GCA_004356175.1_ASM435617v1_genomic.fna/tc_result.tsv
[2023-06-04 21:25:09,521] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:25:09,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:25:09,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/checkm_data
[2023-06-04 21:25:09,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:25:09,543] [INFO] Task started: CheckM
[2023-06-04 21:25:09,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004356175.1_ASM435617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004356175.1_ASM435617v1_genomic.fna/checkm_input GCA_004356175.1_ASM435617v1_genomic.fna/checkm_result
[2023-06-04 21:25:25,852] [INFO] Task succeeded: CheckM
[2023-06-04 21:25:25,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:25:25,880] [INFO] ===== Completeness check finished =====
[2023-06-04 21:25:25,880] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:25:25,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004356175.1_ASM435617v1_genomic.fna/markers.fasta)
[2023-06-04 21:25:25,881] [INFO] Task started: Blastn
[2023-06-04 21:25:25,881] [INFO] Running command: blastn -query GCA_004356175.1_ASM435617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f12a8d7-fd32-4816-a161-39b3ef4dd806/dqc_reference/reference_markers_gtdb.fasta -out GCA_004356175.1_ASM435617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:26,532] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:26,537] [INFO] Selected 9 target genomes.
[2023-06-04 21:25:26,537] [INFO] Target genome list was writen to GCA_004356175.1_ASM435617v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:25:26,603] [INFO] Task started: fastANI
[2023-06-04 21:25:26,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgab4a0237-76b5-43ec-84c4-69378ee52b99/GCA_004356175.1_ASM435617v1_genomic.fna.gz --refList GCA_004356175.1_ASM435617v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004356175.1_ASM435617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:25:31,455] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:31,459] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:25:31,459] [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_004356175.1	s__B3-G11 sp004356175	100.0	285	293	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__B3-G11	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-04 21:25:31,461] [INFO] GTDB search result was written to GCA_004356175.1_ASM435617v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:25:31,462] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:25:31,464] [INFO] DFAST_QC result json was written to GCA_004356175.1_ASM435617v1_genomic.fna/dqc_result.json
[2023-06-04 21:25:31,464] [INFO] DFAST_QC completed!
[2023-06-04 21:25:31,464] [INFO] Total running time: 0h0m35s