[2023-03-17 07:28:31,324] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,324] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference
[2023-03-17 07:28:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stge06a3496-5ad1-49f7-a982-44504198f794/OceanDNA-b37666.fa | prodigal -d OceanDNA-b37666/cds.fna -a OceanDNA-b37666/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:40,186] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:40,186] [INFO] Task started: HMMsearch
[2023-03-17 07:28:40,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b37666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/reference_markers.hmm OceanDNA-b37666/protein.faa > /dev/null
[2023-03-17 07:28:40,428] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:40,429] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge06a3496-5ad1-49f7-a982-44504198f794/OceanDNA-b37666.fa]
[2023-03-17 07:28:40,445] [INFO] Query marker FASTA was written to OceanDNA-b37666/markers.fasta
[2023-03-17 07:28:40,445] [INFO] Task started: Blastn
[2023-03-17 07:28:40,445] [INFO] Running command: blastn -query OceanDNA-b37666/markers.fasta -db /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/reference_markers.fasta -out OceanDNA-b37666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:41,006] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:41,007] [INFO] Selected 20 target genomes.
[2023-03-17 07:28:41,007] [INFO] Target genome list was writen to OceanDNA-b37666/target_genomes.txt
[2023-03-17 07:28:41,023] [INFO] Task started: fastANI
[2023-03-17 07:28:41,023] [INFO] Running command: fastANI --query /var/lib/cwl/stge06a3496-5ad1-49f7-a982-44504198f794/OceanDNA-b37666.fa --refList OceanDNA-b37666/target_genomes.txt --output OceanDNA-b37666/fastani_result.tsv --threads 1
[2023-03-17 07:28:53,165] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:53,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:53,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:53,170] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 07:28:53,170] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 07:28:53,170] [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
Aequoribacter fuscus	strain=IMCC3088	GCA_009910365.1	2518989	2518989	type	True	96.1884	266	278	95	conclusive
Aequoribacter fuscus	strain=IMCC3088	GCA_000204315.2	2518989	2518989	type	True	96.0398	262	278	95	conclusive
--------------------------------------------------------------------------------
[2023-03-17 07:28:53,170] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37666/tc_result.tsv
[2023-03-17 07:28:53,170] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:53,170] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:53,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/checkm_data
[2023-03-17 07:28:53,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:53,174] [INFO] Task started: CheckM
[2023-03-17 07:28:53,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37666/checkm_input OceanDNA-b37666/checkm_result
[2023-03-17 07:29:16,539] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:16,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.84%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:16,541] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:16,541] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:16,542] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37666/markers.fasta)
[2023-03-17 07:29:16,542] [INFO] Task started: Blastn
[2023-03-17 07:29:16,542] [INFO] Running command: blastn -query OceanDNA-b37666/markers.fasta -db /var/lib/cwl/stg45c9f91e-ab8c-48c3-9ae8-11b96e078f84/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:17,373] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:17,374] [INFO] Selected 24 target genomes.
[2023-03-17 07:29:17,374] [INFO] Target genome list was writen to OceanDNA-b37666/target_genomes_gtdb.txt
[2023-03-17 07:29:17,638] [INFO] Task started: fastANI
[2023-03-17 07:29:17,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge06a3496-5ad1-49f7-a982-44504198f794/OceanDNA-b37666.fa --refList OceanDNA-b37666/target_genomes_gtdb.txt --output OceanDNA-b37666/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:30,070] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:30,073] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:30,073] [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
GCF_009910365.1	s__Aequoribacter fuscus	96.1761	267	278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Aequoribacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 07:29:30,073] [INFO] GTDB search result was written to OceanDNA-b37666/result_gtdb.tsv
[2023-03-17 07:29:30,073] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:30,074] [INFO] DFAST_QC result json was written to OceanDNA-b37666/dqc_result.json
[2023-03-17 07:29:30,074] [INFO] DFAST_QC completed!
[2023-03-17 07:29:30,074] [INFO] Total running time: 0h0m59s