[2023-03-18 04:04:53,908] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stga71d874c-3d0c-4b1f-aa4b-becd9c006e4e/OceanDNA-b23517.fa | prodigal -d OceanDNA-b23517/cds.fna -a OceanDNA-b23517/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:05,989] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:05,989] [INFO] Task started: HMMsearch
[2023-03-18 04:05:05,989] [INFO] Running command: hmmsearch --tblout OceanDNA-b23517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/reference_markers.hmm OceanDNA-b23517/protein.faa > /dev/null
[2023-03-18 04:05:06,175] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:06,176] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga71d874c-3d0c-4b1f-aa4b-becd9c006e4e/OceanDNA-b23517.fa]
[2023-03-18 04:05:06,193] [INFO] Query marker FASTA was written to OceanDNA-b23517/markers.fasta
[2023-03-18 04:05:06,194] [INFO] Task started: Blastn
[2023-03-18 04:05:06,194] [INFO] Running command: blastn -query OceanDNA-b23517/markers.fasta -db /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/reference_markers.fasta -out OceanDNA-b23517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:06,806] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:06,807] [INFO] Selected 24 target genomes.
[2023-03-18 04:05:06,807] [INFO] Target genome list was writen to OceanDNA-b23517/target_genomes.txt
[2023-03-18 04:05:06,821] [INFO] Task started: fastANI
[2023-03-18 04:05:06,821] [INFO] Running command: fastANI --query /var/lib/cwl/stga71d874c-3d0c-4b1f-aa4b-becd9c006e4e/OceanDNA-b23517.fa --refList OceanDNA-b23517/target_genomes.txt --output OceanDNA-b23517/fastani_result.tsv --threads 1
[2023-03-18 04:05:20,383] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:20,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:20,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:20,388] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:20,388] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:05:20,389] [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
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	76.3299	58	565	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.2623	58	565	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.0364	54	565	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.0016	57	565	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	75.8097	53	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:20,389] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23517/tc_result.tsv
[2023-03-18 04:05:20,389] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:20,389] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:20,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/checkm_data
[2023-03-18 04:05:20,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:20,485] [INFO] Task started: CheckM
[2023-03-18 04:05:20,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23517/checkm_input OceanDNA-b23517/checkm_result
[2023-03-18 04:05:52,659] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:52,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:52,708] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:52,708] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:52,708] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23517/markers.fasta)
[2023-03-18 04:05:52,709] [INFO] Task started: Blastn
[2023-03-18 04:05:52,710] [INFO] Running command: blastn -query OceanDNA-b23517/markers.fasta -db /var/lib/cwl/stgba4b5f33-424c-4440-a53d-995164a1a823/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:53,764] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:53,769] [INFO] Selected 16 target genomes.
[2023-03-18 04:05:53,769] [INFO] Target genome list was writen to OceanDNA-b23517/target_genomes_gtdb.txt
[2023-03-18 04:05:54,100] [INFO] Task started: fastANI
[2023-03-18 04:05:54,100] [INFO] Running command: fastANI --query /var/lib/cwl/stga71d874c-3d0c-4b1f-aa4b-becd9c006e4e/OceanDNA-b23517.fa --refList OceanDNA-b23517/target_genomes_gtdb.txt --output OceanDNA-b23517/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:02,686] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:02,691] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:06:02,691] [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_013213785.1	s__Henriciella sp013213785	81.9134	447	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854405.1	s__Henriciella sp001854405	77.8222	243	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	77.7923	245	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	77.7798	217	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCA_013213825.1	s__Henriciella sp013213825	77.477	208	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088935.1	s__Henriciella litoralis	76.2623	58	565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:06:02,702] [INFO] GTDB search result was written to OceanDNA-b23517/result_gtdb.tsv
[2023-03-18 04:06:02,702] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:02,704] [INFO] DFAST_QC result json was written to OceanDNA-b23517/dqc_result.json
[2023-03-18 04:06:02,705] [INFO] DFAST_QC completed!
[2023-03-18 04:06:02,705] [INFO] Total running time: 0h1m9s