[2023-03-19 04:59:58,317] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:59:58,317] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:59:58,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference
[2023-03-19 04:59:59,428] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:59:59,429] [INFO] Task started: Prodigal
[2023-03-19 04:59:59,429] [INFO] Running command: cat /var/lib/cwl/stgc218acb9-3480-4812-a326-48c71617e7c2/OceanDNA-b22378.fa | prodigal -d OceanDNA-b22378/cds.fna -a OceanDNA-b22378/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:00:23,060] [INFO] Task succeeded: Prodigal
[2023-03-19 05:00:23,060] [INFO] Task started: HMMsearch
[2023-03-19 05:00:23,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b22378/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/reference_markers.hmm OceanDNA-b22378/protein.faa > /dev/null
[2023-03-19 05:00:23,288] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:00:23,289] [INFO] Found 6/6 markers.
[2023-03-19 05:00:23,322] [INFO] Query marker FASTA was written to OceanDNA-b22378/markers.fasta
[2023-03-19 05:00:23,323] [INFO] Task started: Blastn
[2023-03-19 05:00:23,323] [INFO] Running command: blastn -query OceanDNA-b22378/markers.fasta -db /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/reference_markers.fasta -out OceanDNA-b22378/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:00:23,840] [INFO] Task succeeded: Blastn
[2023-03-19 05:00:23,840] [INFO] Selected 14 target genomes.
[2023-03-19 05:00:23,841] [INFO] Target genome list was writen to OceanDNA-b22378/target_genomes.txt
[2023-03-19 05:00:23,848] [INFO] Task started: fastANI
[2023-03-19 05:00:23,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgc218acb9-3480-4812-a326-48c71617e7c2/OceanDNA-b22378.fa --refList OceanDNA-b22378/target_genomes.txt --output OceanDNA-b22378/fastani_result.tsv --threads 1
[2023-03-19 05:00:39,123] [INFO] Task succeeded: fastANI
[2023-03-19 05:00:39,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:00:39,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:00:39,124] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:00:39,124] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:00:39,124] [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
--------------------------------------------------------------------------------
[2023-03-19 05:00:39,124] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22378/tc_result.tsv
[2023-03-19 05:00:39,124] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:00:39,125] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:00:39,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/checkm_data
[2023-03-19 05:00:39,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:00:39,516] [INFO] Task started: CheckM
[2023-03-19 05:00:39,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22378/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22378/checkm_input OceanDNA-b22378/checkm_result
[2023-03-19 05:01:40,520] [INFO] Task succeeded: CheckM
[2023-03-19 05:01:40,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.42%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:01:40,524] [INFO] ===== Completeness check finished =====
[2023-03-19 05:01:40,524] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:01:40,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22378/markers.fasta)
[2023-03-19 05:01:40,525] [INFO] Task started: Blastn
[2023-03-19 05:01:40,526] [INFO] Running command: blastn -query OceanDNA-b22378/markers.fasta -db /var/lib/cwl/stgcca20d93-61ac-4c18-9aab-db68fe0f8728/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22378/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:41,216] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:41,217] [INFO] Selected 17 target genomes.
[2023-03-19 05:01:41,217] [INFO] Target genome list was writen to OceanDNA-b22378/target_genomes_gtdb.txt
[2023-03-19 05:01:41,236] [INFO] Task started: fastANI
[2023-03-19 05:01:41,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgc218acb9-3480-4812-a326-48c71617e7c2/OceanDNA-b22378.fa --refList OceanDNA-b22378/target_genomes_gtdb.txt --output OceanDNA-b22378/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:01:55,388] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:55,390] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:01:55,390] [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_905480545.1	s__JABAAE01 sp905480545	99.3234	1077	1203	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JABAAE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-19 05:01:55,390] [INFO] GTDB search result was written to OceanDNA-b22378/result_gtdb.tsv
[2023-03-19 05:01:55,390] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:01:55,390] [INFO] DFAST_QC result json was written to OceanDNA-b22378/dqc_result.json
[2023-03-19 05:01:55,391] [INFO] DFAST_QC completed!
[2023-03-19 05:01:55,391] [INFO] Total running time: 0h1m57s