[2023-03-15 10:49:28,604] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,604] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference
[2023-03-15 10:49:29,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,732] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,732] [INFO] Running command: cat /var/lib/cwl/stgf87ff2b8-613b-4b72-a32f-a488b370b21b/OceanDNA-b41971.fa | prodigal -d OceanDNA-b41971/cds.fna -a OceanDNA-b41971/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:35,410] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:35,410] [INFO] Task started: HMMsearch
[2023-03-15 10:49:35,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b41971/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/reference_markers.hmm OceanDNA-b41971/protein.faa > /dev/null
[2023-03-15 10:49:35,573] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:35,574] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf87ff2b8-613b-4b72-a32f-a488b370b21b/OceanDNA-b41971.fa]
[2023-03-15 10:49:35,584] [INFO] Query marker FASTA was written to OceanDNA-b41971/markers.fasta
[2023-03-15 10:49:35,585] [INFO] Task started: Blastn
[2023-03-15 10:49:35,585] [INFO] Running command: blastn -query OceanDNA-b41971/markers.fasta -db /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/reference_markers.fasta -out OceanDNA-b41971/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:36,109] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:36,110] [INFO] Selected 20 target genomes.
[2023-03-15 10:49:36,110] [INFO] Target genome list was writen to OceanDNA-b41971/target_genomes.txt
[2023-03-15 10:49:36,122] [INFO] Task started: fastANI
[2023-03-15 10:49:36,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87ff2b8-613b-4b72-a32f-a488b370b21b/OceanDNA-b41971.fa --refList OceanDNA-b41971/target_genomes.txt --output OceanDNA-b41971/fastani_result.tsv --threads 1
[2023-03-15 10:49:46,391] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:46,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:46,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:46,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:46,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:46,392] [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 10:49:46,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41971/tc_result.tsv
[2023-03-15 10:49:46,392] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:46,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:46,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/checkm_data
[2023-03-15 10:49:46,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:46,397] [INFO] Task started: CheckM
[2023-03-15 10:49:46,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41971/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41971/checkm_input OceanDNA-b41971/checkm_result
[2023-03-15 10:50:07,322] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:07,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.85%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:07,343] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:07,344] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:07,344] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41971/markers.fasta)
[2023-03-15 10:50:07,345] [INFO] Task started: Blastn
[2023-03-15 10:50:07,345] [INFO] Running command: blastn -query OceanDNA-b41971/markers.fasta -db /var/lib/cwl/stg1e40e78b-dfd5-4e3d-a4cd-64e6950330bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41971/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:08,082] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:08,083] [INFO] Selected 6 target genomes.
[2023-03-15 10:50:08,083] [INFO] Target genome list was writen to OceanDNA-b41971/target_genomes_gtdb.txt
[2023-03-15 10:50:08,092] [INFO] Task started: fastANI
[2023-03-15 10:50:08,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87ff2b8-613b-4b72-a32f-a488b370b21b/OceanDNA-b41971.fa --refList OceanDNA-b41971/target_genomes_gtdb.txt --output OceanDNA-b41971/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:09,759] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:09,764] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:50:09,764] [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_902601475.1	s__MED-G82 sp902601475	94.5114	320	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.97	95.73	0.86	0.83	4	-
GCA_902628925.1	s__MED-G82 sp902628925	94.003	323	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331565.1	s__MED-G82 sp003331565	92.8503	184	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594515.1	s__MED-G82 sp902594515	92.6338	310	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	95.37	95.15	0.90	0.90	3	-
GCA_002172535.2	s__MED-G82 sp002172535	92.4142	298	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623535.1	s__MED-G82 sp902623535	92.2114	282	356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G82	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:09,765] [INFO] GTDB search result was written to OceanDNA-b41971/result_gtdb.tsv
[2023-03-15 10:50:09,765] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:09,766] [INFO] DFAST_QC result json was written to OceanDNA-b41971/dqc_result.json
[2023-03-15 10:50:09,766] [INFO] DFAST_QC completed!
[2023-03-15 10:50:09,766] [INFO] Total running time: 0h0m41s