[2023-03-18 22:11:36,994] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:11:36,994] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:11:36,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference
[2023-03-18 22:11:38,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:11:38,078] [INFO] Task started: Prodigal
[2023-03-18 22:11:38,078] [INFO] Running command: cat /var/lib/cwl/stgeae8b17a-2303-40ad-bd8c-8bb9064596b1/OceanDNA-a4761.fa | prodigal -d OceanDNA-a4761/cds.fna -a OceanDNA-a4761/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:11:42,696] [INFO] Task succeeded: Prodigal
[2023-03-18 22:11:42,697] [INFO] Task started: HMMsearch
[2023-03-18 22:11:42,697] [INFO] Running command: hmmsearch --tblout OceanDNA-a4761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/reference_markers.hmm OceanDNA-a4761/protein.faa > /dev/null
[2023-03-18 22:11:42,826] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:11:42,826] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgeae8b17a-2303-40ad-bd8c-8bb9064596b1/OceanDNA-a4761.fa]
[2023-03-18 22:11:42,843] [INFO] Query marker FASTA was written to OceanDNA-a4761/markers.fasta
[2023-03-18 22:11:42,845] [INFO] Task started: Blastn
[2023-03-18 22:11:42,845] [INFO] Running command: blastn -query OceanDNA-a4761/markers.fasta -db /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/reference_markers.fasta -out OceanDNA-a4761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:11:43,305] [INFO] Task succeeded: Blastn
[2023-03-18 22:11:43,312] [INFO] Selected 5 target genomes.
[2023-03-18 22:11:43,313] [INFO] Target genome list was writen to OceanDNA-a4761/target_genomes.txt
[2023-03-18 22:11:43,318] [INFO] Task started: fastANI
[2023-03-18 22:11:43,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgeae8b17a-2303-40ad-bd8c-8bb9064596b1/OceanDNA-a4761.fa --refList OceanDNA-a4761/target_genomes.txt --output OceanDNA-a4761/fastani_result.tsv --threads 1
[2023-03-18 22:11:46,052] [INFO] Task succeeded: fastANI
[2023-03-18 22:11:46,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:11:46,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:11:46,052] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:11:46,052] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:11:46,052] [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
--------------------------------------------------------------------------------
[2023-03-18 22:11:46,053] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4761/tc_result.tsv
[2023-03-18 22:11:46,053] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:11:46,053] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:11:46,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/checkm_data
[2023-03-18 22:11:46,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:11:46,058] [INFO] Task started: CheckM
[2023-03-18 22:11:46,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4761/checkm_input OceanDNA-a4761/checkm_result
[2023-03-18 22:12:04,954] [INFO] Task succeeded: CheckM
[2023-03-18 22:12:04,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.28%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:12:04,965] [INFO] ===== Completeness check finished =====
[2023-03-18 22:12:04,965] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:12:04,965] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4761/markers.fasta)
[2023-03-18 22:12:04,966] [INFO] Task started: Blastn
[2023-03-18 22:12:04,966] [INFO] Running command: blastn -query OceanDNA-a4761/markers.fasta -db /var/lib/cwl/stg7c1288f7-7444-41af-984f-2c2175f2972e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:12:05,483] [INFO] Task succeeded: Blastn
[2023-03-18 22:12:05,484] [INFO] Selected 5 target genomes.
[2023-03-18 22:12:05,484] [INFO] Target genome list was writen to OceanDNA-a4761/target_genomes_gtdb.txt
[2023-03-18 22:12:05,488] [INFO] Task started: fastANI
[2023-03-18 22:12:05,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgeae8b17a-2303-40ad-bd8c-8bb9064596b1/OceanDNA-a4761.fa --refList OceanDNA-a4761/target_genomes_gtdb.txt --output OceanDNA-a4761/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:12:06,655] [INFO] Task succeeded: fastANI
[2023-03-18 22:12:06,657] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:12:06,657] [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_002457195.1	s__MGIIb-P sp002457195	89.0971	115	168	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:12:06,657] [INFO] GTDB search result was written to OceanDNA-a4761/result_gtdb.tsv
[2023-03-18 22:12:06,657] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:12:06,658] [INFO] DFAST_QC result json was written to OceanDNA-a4761/dqc_result.json
[2023-03-18 22:12:06,658] [INFO] DFAST_QC completed!
[2023-03-18 22:12:06,658] [INFO] Total running time: 0h0m30s