[2023-03-17 09:51:05,583] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:51:05,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:51:05,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference
[2023-03-17 09:51:06,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:51:06,664] [INFO] Task started: Prodigal
[2023-03-17 09:51:06,664] [INFO] Running command: cat /var/lib/cwl/stgc0aed27a-68df-4082-ae53-62532de5c619/OceanDNA-b33570.fa | prodigal -d OceanDNA-b33570/cds.fna -a OceanDNA-b33570/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:51:21,620] [INFO] Task succeeded: Prodigal
[2023-03-17 09:51:21,620] [INFO] Task started: HMMsearch
[2023-03-17 09:51:21,620] [INFO] Running command: hmmsearch --tblout OceanDNA-b33570/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/reference_markers.hmm OceanDNA-b33570/protein.faa > /dev/null
[2023-03-17 09:51:21,809] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:51:21,809] [INFO] Found 6/6 markers.
[2023-03-17 09:51:21,825] [INFO] Query marker FASTA was written to OceanDNA-b33570/markers.fasta
[2023-03-17 09:51:21,826] [INFO] Task started: Blastn
[2023-03-17 09:51:21,826] [INFO] Running command: blastn -query OceanDNA-b33570/markers.fasta -db /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/reference_markers.fasta -out OceanDNA-b33570/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:22,379] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:22,379] [INFO] Selected 29 target genomes.
[2023-03-17 09:51:22,380] [INFO] Target genome list was writen to OceanDNA-b33570/target_genomes.txt
[2023-03-17 09:51:22,421] [INFO] Task started: fastANI
[2023-03-17 09:51:22,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aed27a-68df-4082-ae53-62532de5c619/OceanDNA-b33570.fa --refList OceanDNA-b33570/target_genomes.txt --output OceanDNA-b33570/fastani_result.tsv --threads 1
[2023-03-17 09:51:42,319] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:42,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:51:42,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:51:42,320] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:51:42,320] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:51:42,320] [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 09:51:42,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33570/tc_result.tsv
[2023-03-17 09:51:42,320] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:51:42,320] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:51:42,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/checkm_data
[2023-03-17 09:51:42,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:51:42,327] [INFO] Task started: CheckM
[2023-03-17 09:51:42,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33570/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33570/checkm_input OceanDNA-b33570/checkm_result
[2023-03-17 09:52:22,703] [INFO] Task succeeded: CheckM
[2023-03-17 09:52:22,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:52:22,705] [INFO] ===== Completeness check finished =====
[2023-03-17 09:52:22,706] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:52:22,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33570/markers.fasta)
[2023-03-17 09:52:22,707] [INFO] Task started: Blastn
[2023-03-17 09:52:22,707] [INFO] Running command: blastn -query OceanDNA-b33570/markers.fasta -db /var/lib/cwl/stgf0efb020-69ab-4306-92ec-23ced50d5098/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33570/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:52:23,502] [INFO] Task succeeded: Blastn
[2023-03-17 09:52:23,503] [INFO] Selected 30 target genomes.
[2023-03-17 09:52:23,503] [INFO] Target genome list was writen to OceanDNA-b33570/target_genomes_gtdb.txt
[2023-03-17 09:52:24,408] [INFO] Task started: fastANI
[2023-03-17 09:52:24,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aed27a-68df-4082-ae53-62532de5c619/OceanDNA-b33570.fa --refList OceanDNA-b33570/target_genomes_gtdb.txt --output OceanDNA-b33570/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:52:44,162] [INFO] Task succeeded: fastANI
[2023-03-17 09:52:44,166] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:52:44,166] [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_002342365.1	s__UBA3064 sp002342365	99.7791	710	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.81	99.60	0.94	0.90	39	conclusive
GCA_002359635.1	s__UBA3064 sp002359635	77.7849	245	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	99.69	99.55	0.89	0.78	24	-
GCA_016868095.1	s__UBA3064 sp016868095	76.9176	170	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299025.1	s__UBA3064 sp005787245	76.7958	207	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	98.97	98.30	0.89	0.84	12	-
GCA_016868175.1	s__UBA3064 sp016868175	76.322	87	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA3064	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970865.1	s__CAIZPE01 sp018970865	75.7929	50	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:52:44,167] [INFO] GTDB search result was written to OceanDNA-b33570/result_gtdb.tsv
[2023-03-17 09:52:44,167] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:52:44,168] [INFO] DFAST_QC result json was written to OceanDNA-b33570/dqc_result.json
[2023-03-17 09:52:44,168] [INFO] DFAST_QC completed!
[2023-03-17 09:52:44,168] [INFO] Total running time: 0h1m39s