[2023-03-18 08:36:16,004] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,004] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,004] [INFO] DQC Reference Directory: /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,826] [INFO] Running command: cat /var/lib/cwl/stgbd102712-ac38-4544-9d8e-3287be8619ae/OceanDNA-b32697.fa | prodigal -d OceanDNA-b32697/cds.fna -a OceanDNA-b32697/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:35,589] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:35,590] [INFO] Task started: HMMsearch
[2023-03-18 08:36:35,590] [INFO] Running command: hmmsearch --tblout OceanDNA-b32697/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/reference_markers.hmm OceanDNA-b32697/protein.faa > /dev/null
[2023-03-18 08:36:35,813] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:35,813] [INFO] Found 6/6 markers.
[2023-03-18 08:36:35,831] [INFO] Query marker FASTA was written to OceanDNA-b32697/markers.fasta
[2023-03-18 08:36:35,832] [INFO] Task started: Blastn
[2023-03-18 08:36:35,832] [INFO] Running command: blastn -query OceanDNA-b32697/markers.fasta -db /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/reference_markers.fasta -out OceanDNA-b32697/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:36,415] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:36,416] [INFO] Selected 25 target genomes.
[2023-03-18 08:36:36,416] [INFO] Target genome list was writen to OceanDNA-b32697/target_genomes.txt
[2023-03-18 08:36:36,461] [INFO] Task started: fastANI
[2023-03-18 08:36:36,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd102712-ac38-4544-9d8e-3287be8619ae/OceanDNA-b32697.fa --refList OceanDNA-b32697/target_genomes.txt --output OceanDNA-b32697/fastani_result.tsv --threads 1
[2023-03-18 08:36:51,895] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:51,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:51,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:51,896] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:51,896] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:51,896] [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
--------------------------------------------------------------------------------
[2023-03-18 08:36:51,896] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32697/tc_result.tsv
[2023-03-18 08:36:51,896] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:51,896] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:51,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/checkm_data
[2023-03-18 08:36:51,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:51,904] [INFO] Task started: CheckM
[2023-03-18 08:36:51,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32697/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32697/checkm_input OceanDNA-b32697/checkm_result
[2023-03-18 08:37:38,012] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:38,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:38,016] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:38,016] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:38,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32697/markers.fasta)
[2023-03-18 08:37:38,018] [INFO] Task started: Blastn
[2023-03-18 08:37:38,018] [INFO] Running command: blastn -query OceanDNA-b32697/markers.fasta -db /var/lib/cwl/stgda7eb536-e7f4-419c-a4ea-620e50f1847a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32697/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:39,001] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:39,004] [INFO] Selected 23 target genomes.
[2023-03-18 08:37:39,004] [INFO] Target genome list was writen to OceanDNA-b32697/target_genomes_gtdb.txt
[2023-03-18 08:37:39,018] [INFO] Task started: fastANI
[2023-03-18 08:37:39,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd102712-ac38-4544-9d8e-3287be8619ae/OceanDNA-b32697.fa --refList OceanDNA-b32697/target_genomes_gtdb.txt --output OceanDNA-b32697/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:52,662] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:52,664] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:52,664] [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_002348365.1	s__UBA2966 sp002348365	78.6093	518	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__UBA2966	95.0	98.52	97.79	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:52,666] [INFO] GTDB search result was written to OceanDNA-b32697/result_gtdb.tsv
[2023-03-18 08:37:52,668] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:52,670] [INFO] DFAST_QC result json was written to OceanDNA-b32697/dqc_result.json
[2023-03-18 08:37:52,670] [INFO] DFAST_QC completed!
[2023-03-18 08:37:52,670] [INFO] Total running time: 0h1m37s