[2023-06-17 14:43:29,463] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:43:29,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:43:29,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference
[2023-06-17 14:43:31,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:43:31,755] [INFO] Task started: Prodigal
[2023-06-17 14:43:31,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e0668b-1e7f-4cc5-ab19-fb40b4e3e276/GCA_003453025.1_ASM345302v1_genomic.fna.gz | prodigal -d GCA_003453025.1_ASM345302v1_genomic.fna/cds.fna -a GCA_003453025.1_ASM345302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:43:39,351] [INFO] Task succeeded: Prodigal
[2023-06-17 14:43:39,352] [INFO] Task started: HMMsearch
[2023-06-17 14:43:39,352] [INFO] Running command: hmmsearch --tblout GCA_003453025.1_ASM345302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/reference_markers.hmm GCA_003453025.1_ASM345302v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:43:39,593] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:43:39,594] [INFO] Found 6/6 markers.
[2023-06-17 14:43:39,629] [INFO] Query marker FASTA was written to GCA_003453025.1_ASM345302v1_genomic.fna/markers.fasta
[2023-06-17 14:43:39,630] [INFO] Task started: Blastn
[2023-06-17 14:43:39,630] [INFO] Running command: blastn -query GCA_003453025.1_ASM345302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/reference_markers.fasta -out GCA_003453025.1_ASM345302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:40,215] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:40,219] [INFO] Selected 7 target genomes.
[2023-06-17 14:43:40,220] [INFO] Target genome list was writen to GCA_003453025.1_ASM345302v1_genomic.fna/target_genomes.txt
[2023-06-17 14:43:40,222] [INFO] Task started: fastANI
[2023-06-17 14:43:40,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e0668b-1e7f-4cc5-ab19-fb40b4e3e276/GCA_003453025.1_ASM345302v1_genomic.fna.gz --refList GCA_003453025.1_ASM345302v1_genomic.fna/target_genomes.txt --output GCA_003453025.1_ASM345302v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:43:44,681] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:44,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:43:44,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:43:44,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:43:44,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:43:44,686] [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
--------------------------------------------------------------------------------
[2023-06-17 14:43:44,688] [INFO] DFAST Taxonomy check result was written to GCA_003453025.1_ASM345302v1_genomic.fna/tc_result.tsv
[2023-06-17 14:43:44,689] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:43:44,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:43:44,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/checkm_data
[2023-06-17 14:43:44,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:43:44,738] [INFO] Task started: CheckM
[2023-06-17 14:43:44,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003453025.1_ASM345302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003453025.1_ASM345302v1_genomic.fna/checkm_input GCA_003453025.1_ASM345302v1_genomic.fna/checkm_result
[2023-06-17 14:44:12,441] [INFO] Task succeeded: CheckM
[2023-06-17 14:44:12,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:44:12,463] [INFO] ===== Completeness check finished =====
[2023-06-17 14:44:12,463] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:44:12,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003453025.1_ASM345302v1_genomic.fna/markers.fasta)
[2023-06-17 14:44:12,464] [INFO] Task started: Blastn
[2023-06-17 14:44:12,465] [INFO] Running command: blastn -query GCA_003453025.1_ASM345302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddb20188-9ce5-4d67-be65-7cdaede4edd9/dqc_reference/reference_markers_gtdb.fasta -out GCA_003453025.1_ASM345302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:44:13,261] [INFO] Task succeeded: Blastn
[2023-06-17 14:44:13,266] [INFO] Selected 23 target genomes.
[2023-06-17 14:44:13,267] [INFO] Target genome list was writen to GCA_003453025.1_ASM345302v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:44:13,302] [INFO] Task started: fastANI
[2023-06-17 14:44:13,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e0668b-1e7f-4cc5-ab19-fb40b4e3e276/GCA_003453025.1_ASM345302v1_genomic.fna.gz --refList GCA_003453025.1_ASM345302v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003453025.1_ASM345302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:44:26,598] [INFO] Task succeeded: fastANI
[2023-06-17 14:44:26,606] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:44:26,606] [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_002714565.1	s__UBA11883 sp002714565	99.0745	814	876	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA11883	95.0	99.16	99.16	0.92	0.92	2	conclusive
--------------------------------------------------------------------------------
[2023-06-17 14:44:26,608] [INFO] GTDB search result was written to GCA_003453025.1_ASM345302v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:44:26,609] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:44:26,611] [INFO] DFAST_QC result json was written to GCA_003453025.1_ASM345302v1_genomic.fna/dqc_result.json
[2023-06-17 14:44:26,611] [INFO] DFAST_QC completed!
[2023-06-17 14:44:26,611] [INFO] Total running time: 0h0m57s