[2023-03-17 04:48:54,032] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference
[2023-03-17 04:48:55,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,210] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,210] [INFO] Running command: cat /var/lib/cwl/stge1f19828-ee54-4b13-b229-85a3fccb69da/OceanDNA-b39186.fa | prodigal -d OceanDNA-b39186/cds.fna -a OceanDNA-b39186/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:05,177] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:05,177] [INFO] Task started: HMMsearch
[2023-03-17 04:49:05,177] [INFO] Running command: hmmsearch --tblout OceanDNA-b39186/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/reference_markers.hmm OceanDNA-b39186/protein.faa > /dev/null
[2023-03-17 04:49:05,311] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:05,312] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge1f19828-ee54-4b13-b229-85a3fccb69da/OceanDNA-b39186.fa]
[2023-03-17 04:49:05,323] [INFO] Query marker FASTA was written to OceanDNA-b39186/markers.fasta
[2023-03-17 04:49:05,324] [INFO] Task started: Blastn
[2023-03-17 04:49:05,324] [INFO] Running command: blastn -query OceanDNA-b39186/markers.fasta -db /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/reference_markers.fasta -out OceanDNA-b39186/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:05,762] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:05,763] [INFO] Selected 17 target genomes.
[2023-03-17 04:49:05,763] [INFO] Target genome list was writen to OceanDNA-b39186/target_genomes.txt
[2023-03-17 04:49:05,771] [INFO] Task started: fastANI
[2023-03-17 04:49:05,771] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f19828-ee54-4b13-b229-85a3fccb69da/OceanDNA-b39186.fa --refList OceanDNA-b39186/target_genomes.txt --output OceanDNA-b39186/fastani_result.tsv --threads 1
[2023-03-17 04:49:16,858] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:16,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:16,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:16,859] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:16,859] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:16,859] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:16,859] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39186/tc_result.tsv
[2023-03-17 04:49:16,859] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:16,859] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:16,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/checkm_data
[2023-03-17 04:49:16,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:16,865] [INFO] Task started: CheckM
[2023-03-17 04:49:16,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39186/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39186/checkm_input OceanDNA-b39186/checkm_result
[2023-03-17 04:49:45,591] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:45,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:45,593] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:45,593] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:45,593] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39186/markers.fasta)
[2023-03-17 04:49:45,593] [INFO] Task started: Blastn
[2023-03-17 04:49:45,593] [INFO] Running command: blastn -query OceanDNA-b39186/markers.fasta -db /var/lib/cwl/stg4a335180-ecfe-4719-866c-83514e330d31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39186/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:46,002] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:46,003] [INFO] Selected 18 target genomes.
[2023-03-17 04:49:46,003] [INFO] Target genome list was writen to OceanDNA-b39186/target_genomes_gtdb.txt
[2023-03-17 04:49:46,289] [INFO] Task started: fastANI
[2023-03-17 04:49:46,289] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f19828-ee54-4b13-b229-85a3fccb69da/OceanDNA-b39186.fa --refList OceanDNA-b39186/target_genomes_gtdb.txt --output OceanDNA-b39186/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:56,481] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:56,483] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:49:56,483] [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_018662305.1	s__JABJGI01 sp018662305	78.1078	113	562	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__GM7GCV1;g__JABJGI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:56,483] [INFO] GTDB search result was written to OceanDNA-b39186/result_gtdb.tsv
[2023-03-17 04:49:56,484] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:56,484] [INFO] DFAST_QC result json was written to OceanDNA-b39186/dqc_result.json
[2023-03-17 04:49:56,484] [INFO] DFAST_QC completed!
[2023-03-17 04:49:56,484] [INFO] Total running time: 0h1m2s