[2023-03-17 08:11:32,517] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference
[2023-03-17 08:11:33,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,644] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,644] [INFO] Running command: cat /var/lib/cwl/stg5407a0d4-baf9-4186-b59c-82d46edb1d1a/OceanDNA-b36762.fa | prodigal -d OceanDNA-b36762/cds.fna -a OceanDNA-b36762/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:57,815] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:57,816] [INFO] Task started: HMMsearch
[2023-03-17 08:11:57,816] [INFO] Running command: hmmsearch --tblout OceanDNA-b36762/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/reference_markers.hmm OceanDNA-b36762/protein.faa > /dev/null
[2023-03-17 08:11:58,049] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:58,050] [INFO] Found 6/6 markers.
[2023-03-17 08:11:58,081] [INFO] Query marker FASTA was written to OceanDNA-b36762/markers.fasta
[2023-03-17 08:11:58,081] [INFO] Task started: Blastn
[2023-03-17 08:11:58,081] [INFO] Running command: blastn -query OceanDNA-b36762/markers.fasta -db /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/reference_markers.fasta -out OceanDNA-b36762/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:58,736] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:58,737] [INFO] Selected 25 target genomes.
[2023-03-17 08:11:58,737] [INFO] Target genome list was writen to OceanDNA-b36762/target_genomes.txt
[2023-03-17 08:11:58,752] [INFO] Task started: fastANI
[2023-03-17 08:11:58,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg5407a0d4-baf9-4186-b59c-82d46edb1d1a/OceanDNA-b36762.fa --refList OceanDNA-b36762/target_genomes.txt --output OceanDNA-b36762/fastani_result.tsv --threads 1
[2023-03-17 08:12:14,515] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:14,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:14,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:14,519] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:14,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:14,519] [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
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	75.5561	50	1277	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	75.3225	54	1277	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.2775	50	1277	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:14,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36762/tc_result.tsv
[2023-03-17 08:12:14,680] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:14,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:14,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/checkm_data
[2023-03-17 08:12:14,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:14,742] [INFO] Task started: CheckM
[2023-03-17 08:12:14,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36762/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36762/checkm_input OceanDNA-b36762/checkm_result
[2023-03-17 08:13:15,081] [INFO] Task succeeded: CheckM
[2023-03-17 08:13:15,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:13:15,085] [INFO] ===== Completeness check finished =====
[2023-03-17 08:13:15,085] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:13:15,086] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36762/markers.fasta)
[2023-03-17 08:13:15,086] [INFO] Task started: Blastn
[2023-03-17 08:13:15,086] [INFO] Running command: blastn -query OceanDNA-b36762/markers.fasta -db /var/lib/cwl/stg1ffbf0d8-fe51-4e3f-b36c-891fba4015d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36762/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:13:16,221] [INFO] Task succeeded: Blastn
[2023-03-17 08:13:16,223] [INFO] Selected 24 target genomes.
[2023-03-17 08:13:16,223] [INFO] Target genome list was writen to OceanDNA-b36762/target_genomes_gtdb.txt
[2023-03-17 08:13:16,476] [INFO] Task started: fastANI
[2023-03-17 08:13:16,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg5407a0d4-baf9-4186-b59c-82d46edb1d1a/OceanDNA-b36762.fa --refList OceanDNA-b36762/target_genomes_gtdb.txt --output OceanDNA-b36762/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:31,946] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:31,951] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:13:31,951] [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_002728675.1	s__GCA-002728675 sp002728675	99.3847	1138	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002480525.1	s__UBA7803 sp002480525	75.7113	70	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	75.5561	50	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	75.4127	52	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837725.1	s__VXYL01 sp009837725	75.301	89	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	97.81	97.81	0.84	0.84	2	-
GCF_900104805.1	s__Pseudomonas_K oryzae	75.2775	50	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009846005.1	s__VXYL01 sp009846005	75.2686	68	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	99.88	99.87	0.91	0.89	3	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	75.1506	50	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:31,952] [INFO] GTDB search result was written to OceanDNA-b36762/result_gtdb.tsv
[2023-03-17 08:13:31,952] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:31,954] [INFO] DFAST_QC result json was written to OceanDNA-b36762/dqc_result.json
[2023-03-17 08:13:31,954] [INFO] DFAST_QC completed!
[2023-03-17 08:13:31,954] [INFO] Total running time: 0h1m59s