[2023-03-15 09:48:16,400] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,401] [INFO] DQC Reference Directory: /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference
[2023-03-15 09:48:18,054] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stg5391e0c5-9392-44c4-b6d8-ec467da243de/OceanDNA-b39325.fa | prodigal -d OceanDNA-b39325/cds.fna -a OceanDNA-b39325/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:24,161] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:24,161] [INFO] Task started: HMMsearch
[2023-03-15 09:48:24,161] [INFO] Running command: hmmsearch --tblout OceanDNA-b39325/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/reference_markers.hmm OceanDNA-b39325/protein.faa > /dev/null
[2023-03-15 09:48:24,387] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:24,388] [INFO] Found 6/6 markers.
[2023-03-15 09:48:24,399] [INFO] Query marker FASTA was written to OceanDNA-b39325/markers.fasta
[2023-03-15 09:48:24,399] [INFO] Task started: Blastn
[2023-03-15 09:48:24,399] [INFO] Running command: blastn -query OceanDNA-b39325/markers.fasta -db /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/reference_markers.fasta -out OceanDNA-b39325/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:25,068] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:25,069] [INFO] Selected 30 target genomes.
[2023-03-15 09:48:25,069] [INFO] Target genome list was writen to OceanDNA-b39325/target_genomes.txt
[2023-03-15 09:48:25,085] [INFO] Task started: fastANI
[2023-03-15 09:48:25,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg5391e0c5-9392-44c4-b6d8-ec467da243de/OceanDNA-b39325.fa --refList OceanDNA-b39325/target_genomes.txt --output OceanDNA-b39325/fastani_result.tsv --threads 1
[2023-03-15 09:48:44,776] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:44,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:44,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:44,777] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:44,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:44,777] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:44,777] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39325/tc_result.tsv
[2023-03-15 09:48:44,778] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:44,778] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:44,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/checkm_data
[2023-03-15 09:48:44,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:44,783] [INFO] Task started: CheckM
[2023-03-15 09:48:44,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39325/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39325/checkm_input OceanDNA-b39325/checkm_result
[2023-03-15 09:49:05,999] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:05,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:06,001] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:06,001] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:06,002] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39325/markers.fasta)
[2023-03-15 09:49:06,002] [INFO] Task started: Blastn
[2023-03-15 09:49:06,002] [INFO] Running command: blastn -query OceanDNA-b39325/markers.fasta -db /var/lib/cwl/stgf56cf480-5a42-48e1-a7dd-e6aa2764613e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39325/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:06,949] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:06,950] [INFO] Selected 22 target genomes.
[2023-03-15 09:49:06,950] [INFO] Target genome list was writen to OceanDNA-b39325/target_genomes_gtdb.txt
[2023-03-15 09:49:07,419] [INFO] Task started: fastANI
[2023-03-15 09:49:07,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg5391e0c5-9392-44c4-b6d8-ec467da243de/OceanDNA-b39325.fa --refList OceanDNA-b39325/target_genomes_gtdb.txt --output OceanDNA-b39325/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:16,927] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:16,930] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:16,930] [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_002469845.1	s__HTCC2207 sp002469845	80.7063	213	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.61	0.95	0.95	3	-
GCA_018607525.1	s__HTCC2207 sp018607525	79.3526	164	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.00	96.00	0.91	0.91	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	76.8499	52	365	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:16,930] [INFO] GTDB search result was written to OceanDNA-b39325/result_gtdb.tsv
[2023-03-15 09:49:16,931] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:16,931] [INFO] DFAST_QC result json was written to OceanDNA-b39325/dqc_result.json
[2023-03-15 09:49:16,931] [INFO] DFAST_QC completed!
[2023-03-15 09:49:16,931] [INFO] Total running time: 0h1m1s