[2023-03-17 11:25:37,246] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,260] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference
[2023-03-17 11:25:38,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,402] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,402] [INFO] Running command: cat /var/lib/cwl/stgfed58d07-e74c-4904-bb95-1b3017f2351e/OceanDNA-b32481.fa | prodigal -d OceanDNA-b32481/cds.fna -a OceanDNA-b32481/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:42,956] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:42,956] [INFO] Task started: HMMsearch
[2023-03-17 11:25:42,956] [INFO] Running command: hmmsearch --tblout OceanDNA-b32481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/reference_markers.hmm OceanDNA-b32481/protein.faa > /dev/null
[2023-03-17 11:25:43,111] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:43,112] [INFO] Found 6/6 markers.
[2023-03-17 11:25:43,255] [INFO] Query marker FASTA was written to OceanDNA-b32481/markers.fasta
[2023-03-17 11:25:43,255] [INFO] Task started: Blastn
[2023-03-17 11:25:43,256] [INFO] Running command: blastn -query OceanDNA-b32481/markers.fasta -db /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/reference_markers.fasta -out OceanDNA-b32481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:43,743] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:43,792] [INFO] Selected 20 target genomes.
[2023-03-17 11:25:43,792] [INFO] Target genome list was writen to OceanDNA-b32481/target_genomes.txt
[2023-03-17 11:25:43,803] [INFO] Task started: fastANI
[2023-03-17 11:25:43,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed58d07-e74c-4904-bb95-1b3017f2351e/OceanDNA-b32481.fa --refList OceanDNA-b32481/target_genomes.txt --output OceanDNA-b32481/fastani_result.tsv --threads 1
[2023-03-17 11:25:52,688] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:52,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:52,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:52,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:52,688] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:52,689] [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
--------------------------------------------------------------------------------
[2023-03-17 11:25:52,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32481/tc_result.tsv
[2023-03-17 11:25:52,714] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:52,715] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:52,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/checkm_data
[2023-03-17 11:25:52,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:52,723] [INFO] Task started: CheckM
[2023-03-17 11:25:52,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32481/checkm_input OceanDNA-b32481/checkm_result
[2023-03-17 11:26:09,827] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:09,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:10,014] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:10,014] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:10,015] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32481/markers.fasta)
[2023-03-17 11:26:10,016] [INFO] Task started: Blastn
[2023-03-17 11:26:10,016] [INFO] Running command: blastn -query OceanDNA-b32481/markers.fasta -db /var/lib/cwl/stg3e1272d6-608a-442c-bfdf-5a4d15158556/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:10,653] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:10,700] [INFO] Selected 24 target genomes.
[2023-03-17 11:26:10,700] [INFO] Target genome list was writen to OceanDNA-b32481/target_genomes_gtdb.txt
[2023-03-17 11:26:10,725] [INFO] Task started: fastANI
[2023-03-17 11:26:10,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed58d07-e74c-4904-bb95-1b3017f2351e/OceanDNA-b32481.fa --refList OceanDNA-b32481/target_genomes_gtdb.txt --output OceanDNA-b32481/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:15,003] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:15,006] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:26:15,006] [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_002171495.2	s__GCA-2732015 sp002171495	77.9832	50	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690625.1	s__MED722 sp002690625	77.0102	50	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__MED722	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557845.1	s__GCA-2732015 sp902557845	76.2299	50	300	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:15,009] [INFO] GTDB search result was written to OceanDNA-b32481/result_gtdb.tsv
[2023-03-17 11:26:15,009] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:15,012] [INFO] DFAST_QC result json was written to OceanDNA-b32481/dqc_result.json
[2023-03-17 11:26:15,012] [INFO] DFAST_QC completed!
[2023-03-17 11:26:15,012] [INFO] Total running time: 0h0m38s