[2023-03-18 06:30:24,740] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference
[2023-03-18 06:30:25,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,871] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,871] [INFO] Running command: cat /var/lib/cwl/stg9649b44a-aa2a-4147-9d9f-c59b5d0378d3/OceanDNA-b25382.fa | prodigal -d OceanDNA-b25382/cds.fna -a OceanDNA-b25382/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:28,867] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:28,868] [INFO] Task started: HMMsearch
[2023-03-18 06:30:28,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b25382/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/reference_markers.hmm OceanDNA-b25382/protein.faa > /dev/null
[2023-03-18 06:30:29,040] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:29,041] [INFO] Found 6/6 markers.
[2023-03-18 06:30:29,050] [INFO] Query marker FASTA was written to OceanDNA-b25382/markers.fasta
[2023-03-18 06:30:29,050] [INFO] Task started: Blastn
[2023-03-18 06:30:29,050] [INFO] Running command: blastn -query OceanDNA-b25382/markers.fasta -db /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/reference_markers.fasta -out OceanDNA-b25382/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:29,753] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:29,760] [INFO] Selected 18 target genomes.
[2023-03-18 06:30:29,761] [INFO] Target genome list was writen to OceanDNA-b25382/target_genomes.txt
[2023-03-18 06:30:30,043] [INFO] Task started: fastANI
[2023-03-18 06:30:30,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg9649b44a-aa2a-4147-9d9f-c59b5d0378d3/OceanDNA-b25382.fa --refList OceanDNA-b25382/target_genomes.txt --output OceanDNA-b25382/fastani_result.tsv --threads 1
[2023-03-18 06:30:37,505] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:37,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:37,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:37,508] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:37,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:30:37,508] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	75.8839	51	150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:30:37,511] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25382/tc_result.tsv
[2023-03-18 06:30:37,514] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:37,515] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:37,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/checkm_data
[2023-03-18 06:30:37,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:37,543] [INFO] Task started: CheckM
[2023-03-18 06:30:37,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25382/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25382/checkm_input OceanDNA-b25382/checkm_result
[2023-03-18 06:30:54,388] [INFO] Task succeeded: CheckM
[2023-03-18 06:30:54,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.77%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:30:54,481] [INFO] ===== Completeness check finished =====
[2023-03-18 06:30:54,481] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:30:54,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25382/markers.fasta)
[2023-03-18 06:30:54,483] [INFO] Task started: Blastn
[2023-03-18 06:30:54,483] [INFO] Running command: blastn -query OceanDNA-b25382/markers.fasta -db /var/lib/cwl/stg1e86cfad-91d1-41bc-aa68-3bd2da71c2e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25382/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:55,864] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:55,872] [INFO] Selected 21 target genomes.
[2023-03-18 06:30:55,872] [INFO] Target genome list was writen to OceanDNA-b25382/target_genomes_gtdb.txt
[2023-03-18 06:30:56,165] [INFO] Task started: fastANI
[2023-03-18 06:30:56,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg9649b44a-aa2a-4147-9d9f-c59b5d0378d3/OceanDNA-b25382.fa --refList OceanDNA-b25382/target_genomes_gtdb.txt --output OceanDNA-b25382/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:30:59,678] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:59,682] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:30:59,682] [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_000513055.1	s__AAA240-E13 sp000513055	77.7887	50	150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000504625.1	s__AAA240-E13 sp000504625	77.396	50	150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211695.1	s__AAA240-E13 sp003211695	77.3096	60	150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002689925.1	s__GCA-2689925 sp002689925	76.794	53	150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__GCA-2689925	95.0	99.81	99.81	0.69	0.69	2	-
GCA_902634485.1	s__Pelagibacter sp902634485	76.1909	50	150	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:30:59,686] [INFO] GTDB search result was written to OceanDNA-b25382/result_gtdb.tsv
[2023-03-18 06:30:59,690] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:30:59,696] [INFO] DFAST_QC result json was written to OceanDNA-b25382/dqc_result.json
[2023-03-18 06:30:59,696] [INFO] DFAST_QC completed!
[2023-03-18 06:30:59,696] [INFO] Total running time: 0h0m35s