[2023-03-16 02:38:04,741] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,741] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,741] [INFO] DQC Reference Directory: /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference
[2023-03-16 02:38:05,900] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:05,901] [INFO] Task started: Prodigal
[2023-03-16 02:38:05,901] [INFO] Running command: cat /var/lib/cwl/stg4d9e5b43-6c78-41f4-bd93-bd2baa684f0f/OceanDNA-b13824.fa | prodigal -d OceanDNA-b13824/cds.fna -a OceanDNA-b13824/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:12,625] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:12,626] [INFO] Task started: HMMsearch
[2023-03-16 02:38:12,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b13824/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/reference_markers.hmm OceanDNA-b13824/protein.faa > /dev/null
[2023-03-16 02:38:12,788] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:12,789] [INFO] Found 6/6 markers.
[2023-03-16 02:38:12,798] [INFO] Query marker FASTA was written to OceanDNA-b13824/markers.fasta
[2023-03-16 02:38:12,798] [INFO] Task started: Blastn
[2023-03-16 02:38:12,798] [INFO] Running command: blastn -query OceanDNA-b13824/markers.fasta -db /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/reference_markers.fasta -out OceanDNA-b13824/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:13,294] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:13,295] [INFO] Selected 14 target genomes.
[2023-03-16 02:38:13,295] [INFO] Target genome list was writen to OceanDNA-b13824/target_genomes.txt
[2023-03-16 02:38:13,302] [INFO] Task started: fastANI
[2023-03-16 02:38:13,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9e5b43-6c78-41f4-bd93-bd2baa684f0f/OceanDNA-b13824.fa --refList OceanDNA-b13824/target_genomes.txt --output OceanDNA-b13824/fastani_result.tsv --threads 1
[2023-03-16 02:38:18,992] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:18,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:18,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:18,993] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:18,993] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:18,993] [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
--------------------------------------------------------------------------------
[2023-03-16 02:38:18,993] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13824/tc_result.tsv
[2023-03-16 02:38:18,993] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:18,993] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:18,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/checkm_data
[2023-03-16 02:38:18,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:18,998] [INFO] Task started: CheckM
[2023-03-16 02:38:18,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13824/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13824/checkm_input OceanDNA-b13824/checkm_result
[2023-03-16 02:38:40,821] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:40,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:40,823] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:40,823] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:40,824] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13824/markers.fasta)
[2023-03-16 02:38:40,824] [INFO] Task started: Blastn
[2023-03-16 02:38:40,824] [INFO] Running command: blastn -query OceanDNA-b13824/markers.fasta -db /var/lib/cwl/stge7390e49-c610-491a-98ae-4d2053367687/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13824/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:41,599] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:41,599] [INFO] Selected 15 target genomes.
[2023-03-16 02:38:41,599] [INFO] Target genome list was writen to OceanDNA-b13824/target_genomes_gtdb.txt
[2023-03-16 02:38:42,051] [INFO] Task started: fastANI
[2023-03-16 02:38:42,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9e5b43-6c78-41f4-bd93-bd2baa684f0f/OceanDNA-b13824.fa --refList OceanDNA-b13824/target_genomes_gtdb.txt --output OceanDNA-b13824/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:38:46,330] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:46,333] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:38:46,333] [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_009392295.1	s__GCA-2719675 sp009392295	99.9603	416	430	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-2719675;g__GCA-2719675	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002719675.1	s__GCA-2719675 sp002719675	82.4181	320	430	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-2719675;g__GCA-2719675	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:38:46,333] [INFO] GTDB search result was written to OceanDNA-b13824/result_gtdb.tsv
[2023-03-16 02:38:46,333] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:38:46,334] [INFO] DFAST_QC result json was written to OceanDNA-b13824/dqc_result.json
[2023-03-16 02:38:46,334] [INFO] DFAST_QC completed!
[2023-03-16 02:38:46,334] [INFO] Total running time: 0h0m42s