[2023-03-17 13:01:52,508] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:52,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:52,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference
[2023-03-17 13:01:55,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:55,105] [INFO] Task started: Prodigal
[2023-03-17 13:01:55,105] [INFO] Running command: cat /var/lib/cwl/stgf1ba188c-4dd6-4849-a78e-8d371c00ec60/OceanDNA-b37260.fa | prodigal -d OceanDNA-b37260/cds.fna -a OceanDNA-b37260/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:09,060] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:09,060] [INFO] Task started: HMMsearch
[2023-03-17 13:02:09,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b37260/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/reference_markers.hmm OceanDNA-b37260/protein.faa > /dev/null
[2023-03-17 13:02:09,260] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:09,260] [INFO] Found 6/6 markers.
[2023-03-17 13:02:09,281] [INFO] Query marker FASTA was written to OceanDNA-b37260/markers.fasta
[2023-03-17 13:02:09,282] [INFO] Task started: Blastn
[2023-03-17 13:02:09,282] [INFO] Running command: blastn -query OceanDNA-b37260/markers.fasta -db /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/reference_markers.fasta -out OceanDNA-b37260/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:09,845] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:09,846] [INFO] Selected 21 target genomes.
[2023-03-17 13:02:09,846] [INFO] Target genome list was writen to OceanDNA-b37260/target_genomes.txt
[2023-03-17 13:02:09,859] [INFO] Task started: fastANI
[2023-03-17 13:02:09,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ba188c-4dd6-4849-a78e-8d371c00ec60/OceanDNA-b37260.fa --refList OceanDNA-b37260/target_genomes.txt --output OceanDNA-b37260/fastani_result.tsv --threads 1
[2023-03-17 13:02:23,689] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:23,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:23,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:23,690] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:23,690] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:23,690] [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 13:02:23,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37260/tc_result.tsv
[2023-03-17 13:02:23,690] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:23,690] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:23,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/checkm_data
[2023-03-17 13:02:23,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:23,698] [INFO] Task started: CheckM
[2023-03-17 13:02:23,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37260/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37260/checkm_input OceanDNA-b37260/checkm_result
[2023-03-17 13:03:07,658] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:07,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:07,665] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:07,665] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:07,665] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37260/markers.fasta)
[2023-03-17 13:03:07,666] [INFO] Task started: Blastn
[2023-03-17 13:03:07,666] [INFO] Running command: blastn -query OceanDNA-b37260/markers.fasta -db /var/lib/cwl/stgcb5c9feb-8218-4294-893d-679de9d0d6e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37260/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:08,677] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:08,678] [INFO] Selected 24 target genomes.
[2023-03-17 13:03:08,678] [INFO] Target genome list was writen to OceanDNA-b37260/target_genomes_gtdb.txt
[2023-03-17 13:03:09,073] [INFO] Task started: fastANI
[2023-03-17 13:03:09,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1ba188c-4dd6-4849-a78e-8d371c00ec60/OceanDNA-b37260.fa --refList OceanDNA-b37260/target_genomes_gtdb.txt --output OceanDNA-b37260/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:23,636] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:23,638] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:03:23,638] [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_002712135.1	s__UBA7455 sp002712135	99.1858	700	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7455	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003452295.1	s__UBA7455 sp003452295	81.3904	400	803	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7455	95.0	99.39	99.39	0.69	0.69	2	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:23,639] [INFO] GTDB search result was written to OceanDNA-b37260/result_gtdb.tsv
[2023-03-17 13:03:23,639] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:23,639] [INFO] DFAST_QC result json was written to OceanDNA-b37260/dqc_result.json
[2023-03-17 13:03:23,639] [INFO] DFAST_QC completed!
[2023-03-17 13:03:23,639] [INFO] Total running time: 0h1m31s