[2023-03-16 20:07:31,796] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:07:31,796] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:07:31,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference
[2023-03-16 20:07:32,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:07:32,926] [INFO] Task started: Prodigal
[2023-03-16 20:07:32,926] [INFO] Running command: cat /var/lib/cwl/stg66b0385a-9539-484e-9d78-5da3a4ae1184/OceanDNA-b45648.fa | prodigal -d OceanDNA-b45648/cds.fna -a OceanDNA-b45648/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:07:41,990] [INFO] Task succeeded: Prodigal
[2023-03-16 20:07:41,991] [INFO] Task started: HMMsearch
[2023-03-16 20:07:41,991] [INFO] Running command: hmmsearch --tblout OceanDNA-b45648/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/reference_markers.hmm OceanDNA-b45648/protein.faa > /dev/null
[2023-03-16 20:07:42,131] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:07:42,132] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg66b0385a-9539-484e-9d78-5da3a4ae1184/OceanDNA-b45648.fa]
[2023-03-16 20:07:42,145] [INFO] Query marker FASTA was written to OceanDNA-b45648/markers.fasta
[2023-03-16 20:07:42,147] [INFO] Task started: Blastn
[2023-03-16 20:07:42,147] [INFO] Running command: blastn -query OceanDNA-b45648/markers.fasta -db /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/reference_markers.fasta -out OceanDNA-b45648/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:07:42,627] [INFO] Task succeeded: Blastn
[2023-03-16 20:07:42,628] [INFO] Selected 2 target genomes.
[2023-03-16 20:07:42,628] [INFO] Target genome list was writen to OceanDNA-b45648/target_genomes.txt
[2023-03-16 20:07:42,631] [INFO] Task started: fastANI
[2023-03-16 20:07:42,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b0385a-9539-484e-9d78-5da3a4ae1184/OceanDNA-b45648.fa --refList OceanDNA-b45648/target_genomes.txt --output OceanDNA-b45648/fastani_result.tsv --threads 1
[2023-03-16 20:07:43,067] [INFO] Task succeeded: fastANI
[2023-03-16 20:07:43,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:07:43,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:07:43,067] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:07:43,068] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 20:07:43,068] [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 20:07:43,068] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45648/tc_result.tsv
[2023-03-16 20:07:43,068] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:07:43,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:07:43,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/checkm_data
[2023-03-16 20:07:43,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:07:43,134] [INFO] Task started: CheckM
[2023-03-16 20:07:43,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45648/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45648/checkm_input OceanDNA-b45648/checkm_result
[2023-03-16 20:08:11,940] [INFO] Task succeeded: CheckM
[2023-03-16 20:08:11,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 20:08:11,943] [INFO] ===== Completeness check finished =====
[2023-03-16 20:08:11,943] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:08:11,943] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45648/markers.fasta)
[2023-03-16 20:08:11,945] [INFO] Task started: Blastn
[2023-03-16 20:08:11,945] [INFO] Running command: blastn -query OceanDNA-b45648/markers.fasta -db /var/lib/cwl/stgce76a00a-b0d1-4f38-a455-6515f6ed254e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45648/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:08:12,518] [INFO] Task succeeded: Blastn
[2023-03-16 20:08:12,519] [INFO] Selected 12 target genomes.
[2023-03-16 20:08:12,519] [INFO] Target genome list was writen to OceanDNA-b45648/target_genomes_gtdb.txt
[2023-03-16 20:08:12,533] [INFO] Task started: fastANI
[2023-03-16 20:08:12,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b0385a-9539-484e-9d78-5da3a4ae1184/OceanDNA-b45648.fa --refList OceanDNA-b45648/target_genomes_gtdb.txt --output OceanDNA-b45648/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:08:17,642] [INFO] Task succeeded: fastANI
[2023-03-16 20:08:17,645] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:08:17,645] [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_002171765.1	s__MB11C04 sp002171765	92.2186	164	259	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.33	98.33	0.72	0.72	2	-
GCA_002364975.1	s__MB11C04 sp002364975	91.5961	227	259	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.20	99.18	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-16 20:08:17,645] [INFO] GTDB search result was written to OceanDNA-b45648/result_gtdb.tsv
[2023-03-16 20:08:17,646] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:08:17,647] [INFO] DFAST_QC result json was written to OceanDNA-b45648/dqc_result.json
[2023-03-16 20:08:17,647] [INFO] DFAST_QC completed!
[2023-03-16 20:08:17,647] [INFO] Total running time: 0h0m46s