[2023-03-14 12:28:23,291] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:28:23,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:28:23,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference
[2023-03-14 12:28:25,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:28:25,336] [INFO] Task started: Prodigal
[2023-03-14 12:28:25,337] [INFO] Running command: cat /var/lib/cwl/stg51c0566e-641c-42c0-8b4e-ae9512ed0ad2/OceanDNA-b40628.fa | prodigal -d OceanDNA-b40628/cds.fna -a OceanDNA-b40628/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:28:35,368] [INFO] Task succeeded: Prodigal
[2023-03-14 12:28:35,368] [INFO] Task started: HMMsearch
[2023-03-14 12:28:35,368] [INFO] Running command: hmmsearch --tblout OceanDNA-b40628/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/reference_markers.hmm OceanDNA-b40628/protein.faa > /dev/null
[2023-03-14 12:28:35,684] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:28:35,685] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg51c0566e-641c-42c0-8b4e-ae9512ed0ad2/OceanDNA-b40628.fa]
[2023-03-14 12:28:35,708] [INFO] Query marker FASTA was written to OceanDNA-b40628/markers.fasta
[2023-03-14 12:28:35,710] [INFO] Task started: Blastn
[2023-03-14 12:28:35,710] [INFO] Running command: blastn -query OceanDNA-b40628/markers.fasta -db /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/reference_markers.fasta -out OceanDNA-b40628/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:28:39,286] [INFO] Task succeeded: Blastn
[2023-03-14 12:28:39,287] [INFO] Selected 9 target genomes.
[2023-03-14 12:28:39,287] [INFO] Target genome list was writen to OceanDNA-b40628/target_genomes.txt
[2023-03-14 12:28:39,294] [INFO] Task started: fastANI
[2023-03-14 12:28:39,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c0566e-641c-42c0-8b4e-ae9512ed0ad2/OceanDNA-b40628.fa --refList OceanDNA-b40628/target_genomes.txt --output OceanDNA-b40628/fastani_result.tsv --threads 1
[2023-03-14 12:28:46,100] [INFO] Task succeeded: fastANI
[2023-03-14 12:28:46,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:28:46,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:28:46,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:28:46,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:28:46,101] [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
--------------------------------------------------------------------------------
[2023-03-14 12:28:46,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40628/tc_result.tsv
[2023-03-14 12:28:46,418] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:28:46,418] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:28:46,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/checkm_data
[2023-03-14 12:28:46,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:28:46,525] [INFO] Task started: CheckM
[2023-03-14 12:28:46,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40628/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40628/checkm_input OceanDNA-b40628/checkm_result
[2023-03-14 12:29:15,562] [INFO] Task succeeded: CheckM
[2023-03-14 12:29:15,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.99%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:29:15,566] [INFO] ===== Completeness check finished =====
[2023-03-14 12:29:15,566] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:29:15,566] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40628/markers.fasta)
[2023-03-14 12:29:15,567] [INFO] Task started: Blastn
[2023-03-14 12:29:15,567] [INFO] Running command: blastn -query OceanDNA-b40628/markers.fasta -db /var/lib/cwl/stgcb33b49a-8457-4ac0-a014-8a9c771a3e2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40628/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:29:16,220] [INFO] Task succeeded: Blastn
[2023-03-14 12:29:16,221] [INFO] Selected 14 target genomes.
[2023-03-14 12:29:16,222] [INFO] Target genome list was writen to OceanDNA-b40628/target_genomes_gtdb.txt
[2023-03-14 12:29:16,238] [INFO] Task started: fastANI
[2023-03-14 12:29:16,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c0566e-641c-42c0-8b4e-ae9512ed0ad2/OceanDNA-b40628.fa --refList OceanDNA-b40628/target_genomes_gtdb.txt --output OceanDNA-b40628/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:29:24,065] [INFO] Task succeeded: fastANI
[2023-03-14 12:29:24,069] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:29:24,069] [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_002401885.1	s__UBA9145 sp002401885	85.0293	444	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762975.1	s__UBA9145 sp016762975	82.7168	356	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	82.5325	377	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_905478195.1	s__UBA9145 sp003483155	77.9937	188	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_013204155.1	s__UBA9145 sp013204155	76.1592	51	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:29:24,070] [INFO] GTDB search result was written to OceanDNA-b40628/result_gtdb.tsv
[2023-03-14 12:29:24,070] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:29:24,071] [INFO] DFAST_QC result json was written to OceanDNA-b40628/dqc_result.json
[2023-03-14 12:29:24,071] [INFO] DFAST_QC completed!
[2023-03-14 12:29:24,072] [INFO] Total running time: 0h1m1s