[2023-03-18 06:15:37,957] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:15:37,957] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:15:37,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference
[2023-03-18 06:15:39,042] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:15:39,042] [INFO] Task started: Prodigal
[2023-03-18 06:15:39,042] [INFO] Running command: cat /var/lib/cwl/stgfc7488ae-3d9a-4a5a-8f07-794e2578b094/OceanDNA-b32730.fa | prodigal -d OceanDNA-b32730/cds.fna -a OceanDNA-b32730/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:15:50,290] [INFO] Task succeeded: Prodigal
[2023-03-18 06:15:50,291] [INFO] Task started: HMMsearch
[2023-03-18 06:15:50,291] [INFO] Running command: hmmsearch --tblout OceanDNA-b32730/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/reference_markers.hmm OceanDNA-b32730/protein.faa > /dev/null
[2023-03-18 06:15:50,468] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:15:50,468] [INFO] Found 6/6 markers.
[2023-03-18 06:15:50,482] [INFO] Query marker FASTA was written to OceanDNA-b32730/markers.fasta
[2023-03-18 06:15:50,483] [INFO] Task started: Blastn
[2023-03-18 06:15:50,484] [INFO] Running command: blastn -query OceanDNA-b32730/markers.fasta -db /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/reference_markers.fasta -out OceanDNA-b32730/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:15:51,041] [INFO] Task succeeded: Blastn
[2023-03-18 06:15:51,041] [INFO] Selected 11 target genomes.
[2023-03-18 06:15:51,042] [INFO] Target genome list was writen to OceanDNA-b32730/target_genomes.txt
[2023-03-18 06:15:51,049] [INFO] Task started: fastANI
[2023-03-18 06:15:51,049] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7488ae-3d9a-4a5a-8f07-794e2578b094/OceanDNA-b32730.fa --refList OceanDNA-b32730/target_genomes.txt --output OceanDNA-b32730/fastani_result.tsv --threads 1
[2023-03-18 06:15:56,701] [INFO] Task succeeded: fastANI
[2023-03-18 06:15:56,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:15:56,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:15:56,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:15:56,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:15:56,702] [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 06:15:56,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32730/tc_result.tsv
[2023-03-18 06:15:56,702] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:15:56,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:15:56,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/checkm_data
[2023-03-18 06:15:56,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:15:56,748] [INFO] Task started: CheckM
[2023-03-18 06:15:56,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32730/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32730/checkm_input OceanDNA-b32730/checkm_result
[2023-03-18 06:16:28,609] [INFO] Task succeeded: CheckM
[2023-03-18 06:16:28,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:16:28,619] [INFO] ===== Completeness check finished =====
[2023-03-18 06:16:28,620] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:16:28,620] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32730/markers.fasta)
[2023-03-18 06:16:28,621] [INFO] Task started: Blastn
[2023-03-18 06:16:28,621] [INFO] Running command: blastn -query OceanDNA-b32730/markers.fasta -db /var/lib/cwl/stg95721fef-45dd-4143-8bab-b20bd8d776d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32730/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:16:29,530] [INFO] Task succeeded: Blastn
[2023-03-18 06:16:29,537] [INFO] Selected 24 target genomes.
[2023-03-18 06:16:29,537] [INFO] Target genome list was writen to OceanDNA-b32730/target_genomes_gtdb.txt
[2023-03-18 06:16:29,858] [INFO] Task started: fastANI
[2023-03-18 06:16:29,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7488ae-3d9a-4a5a-8f07-794e2578b094/OceanDNA-b32730.fa --refList OceanDNA-b32730/target_genomes_gtdb.txt --output OceanDNA-b32730/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:16:36,035] [INFO] Task succeeded: fastANI
[2023-03-18 06:16:36,037] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:16:36,037] [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_002713365.1	s__UBA6615 sp002713365	84.0655	649	719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA6615	95.0	98.47	98.47	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 06:16:36,040] [INFO] GTDB search result was written to OceanDNA-b32730/result_gtdb.tsv
[2023-03-18 06:16:36,041] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:16:36,041] [INFO] DFAST_QC result json was written to OceanDNA-b32730/dqc_result.json
[2023-03-18 06:16:36,041] [INFO] DFAST_QC completed!
[2023-03-18 06:16:36,041] [INFO] Total running time: 0h0m58s