[2023-03-16 07:55:45,194] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,195] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stgbc382e0e-3f90-428f-b405-a3de127b2ca9/OceanDNA-b25524.fa | prodigal -d OceanDNA-b25524/cds.fna -a OceanDNA-b25524/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:55:50,513] [INFO] Task succeeded: Prodigal
[2023-03-16 07:55:50,513] [INFO] Task started: HMMsearch
[2023-03-16 07:55:50,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b25524/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/reference_markers.hmm OceanDNA-b25524/protein.faa > /dev/null
[2023-03-16 07:55:50,689] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:55:50,690] [INFO] Found 6/6 markers.
[2023-03-16 07:55:50,697] [INFO] Query marker FASTA was written to OceanDNA-b25524/markers.fasta
[2023-03-16 07:55:50,699] [INFO] Task started: Blastn
[2023-03-16 07:55:50,699] [INFO] Running command: blastn -query OceanDNA-b25524/markers.fasta -db /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/reference_markers.fasta -out OceanDNA-b25524/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:55:51,422] [INFO] Task succeeded: Blastn
[2023-03-16 07:55:51,422] [INFO] Selected 13 target genomes.
[2023-03-16 07:55:51,423] [INFO] Target genome list was writen to OceanDNA-b25524/target_genomes.txt
[2023-03-16 07:55:51,431] [INFO] Task started: fastANI
[2023-03-16 07:55:51,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc382e0e-3f90-428f-b405-a3de127b2ca9/OceanDNA-b25524.fa --refList OceanDNA-b25524/target_genomes.txt --output OceanDNA-b25524/fastani_result.tsv --threads 1
[2023-03-16 07:55:56,100] [INFO] Task succeeded: fastANI
[2023-03-16 07:55:56,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:55:56,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:55:56,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:55:56,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:55:56,101] [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 07:55:56,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25524/tc_result.tsv
[2023-03-16 07:55:56,101] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:55:56,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:55:56,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/checkm_data
[2023-03-16 07:55:56,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:55:56,107] [INFO] Task started: CheckM
[2023-03-16 07:55:56,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25524/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25524/checkm_input OceanDNA-b25524/checkm_result
[2023-03-16 07:56:17,635] [INFO] Task succeeded: CheckM
[2023-03-16 07:56:17,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:56:17,637] [INFO] ===== Completeness check finished =====
[2023-03-16 07:56:17,637] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:56:17,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25524/markers.fasta)
[2023-03-16 07:56:17,639] [INFO] Task started: Blastn
[2023-03-16 07:56:17,639] [INFO] Running command: blastn -query OceanDNA-b25524/markers.fasta -db /var/lib/cwl/stg589f7915-69f3-43e0-bb80-0389ae596f5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25524/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:18,796] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:18,797] [INFO] Selected 15 target genomes.
[2023-03-16 07:56:18,797] [INFO] Target genome list was writen to OceanDNA-b25524/target_genomes_gtdb.txt
[2023-03-16 07:56:19,114] [INFO] Task started: fastANI
[2023-03-16 07:56:19,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc382e0e-3f90-428f-b405-a3de127b2ca9/OceanDNA-b25524.fa --refList OceanDNA-b25524/target_genomes_gtdb.txt --output OceanDNA-b25524/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:56:21,822] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:21,826] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:56:21,827] [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_002684895.1	s__HIMB114 sp002684895	96.53	169	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	97.17	97.17	0.86	0.86	2	conclusive
GCA_902524955.1	s__HIMB114 sp902524955	83.9899	160	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692055.1	s__HIMB114 sp002692055	83.6564	118	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.96	99.96	0.77	0.77	2	-
GCA_002171085.1	s__HIMB114 sp002171085	79.3344	98	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.62	99.25	0.83	0.70	3	-
GCA_000163555.2	s__HIMB114 sp000163555	78.9334	128	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638005.1	s__HIMB114 sp008638005	77.8153	88	196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:56:21,827] [INFO] GTDB search result was written to OceanDNA-b25524/result_gtdb.tsv
[2023-03-16 07:56:21,827] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:56:21,828] [INFO] DFAST_QC result json was written to OceanDNA-b25524/dqc_result.json
[2023-03-16 07:56:21,828] [INFO] DFAST_QC completed!
[2023-03-16 07:56:21,828] [INFO] Total running time: 0h0m37s