[2023-03-18 21:15:29,376] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,378] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference
[2023-03-18 21:15:31,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,047] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,047] [INFO] Running command: cat /var/lib/cwl/stg3fa4d633-7cbe-42a4-98df-3699ff425152/OceanDNA-b4060.fa | prodigal -d OceanDNA-b4060/cds.fna -a OceanDNA-b4060/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:46,267] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:46,268] [INFO] Task started: HMMsearch
[2023-03-18 21:15:46,268] [INFO] Running command: hmmsearch --tblout OceanDNA-b4060/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/reference_markers.hmm OceanDNA-b4060/protein.faa > /dev/null
[2023-03-18 21:15:46,475] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:46,476] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3fa4d633-7cbe-42a4-98df-3699ff425152/OceanDNA-b4060.fa]
[2023-03-18 21:15:46,505] [INFO] Query marker FASTA was written to OceanDNA-b4060/markers.fasta
[2023-03-18 21:15:46,506] [INFO] Task started: Blastn
[2023-03-18 21:15:46,506] [INFO] Running command: blastn -query OceanDNA-b4060/markers.fasta -db /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/reference_markers.fasta -out OceanDNA-b4060/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:47,003] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:47,008] [INFO] Selected 14 target genomes.
[2023-03-18 21:15:47,009] [INFO] Target genome list was writen to OceanDNA-b4060/target_genomes.txt
[2023-03-18 21:15:47,016] [INFO] Task started: fastANI
[2023-03-18 21:15:47,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa4d633-7cbe-42a4-98df-3699ff425152/OceanDNA-b4060.fa --refList OceanDNA-b4060/target_genomes.txt --output OceanDNA-b4060/fastani_result.tsv --threads 1
[2023-03-18 21:15:55,652] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:55,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:55,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:55,656] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:55,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:15:55,656] [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
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	78.2225	132	422	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:15:55,658] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4060/tc_result.tsv
[2023-03-18 21:15:55,661] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:55,661] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:55,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/checkm_data
[2023-03-18 21:15:55,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:55,668] [INFO] Task started: CheckM
[2023-03-18 21:15:55,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4060/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4060/checkm_input OceanDNA-b4060/checkm_result
[2023-03-18 21:16:39,068] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:39,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:39,081] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:39,081] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:39,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4060/markers.fasta)
[2023-03-18 21:16:39,083] [INFO] Task started: Blastn
[2023-03-18 21:16:39,083] [INFO] Running command: blastn -query OceanDNA-b4060/markers.fasta -db /var/lib/cwl/stgf80a8e61-1e00-4180-b38d-6f898df32fc4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4060/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:39,683] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:39,688] [INFO] Selected 22 target genomes.
[2023-03-18 21:16:39,689] [INFO] Target genome list was writen to OceanDNA-b4060/target_genomes_gtdb.txt
[2023-03-18 21:16:39,715] [INFO] Task started: fastANI
[2023-03-18 21:16:39,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa4d633-7cbe-42a4-98df-3699ff425152/OceanDNA-b4060.fa --refList OceanDNA-b4060/target_genomes_gtdb.txt --output OceanDNA-b4060/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:53,018] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:53,022] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:53,022] [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
GCF_001747105.1	s__Fabibacter misakiensis	78.2512	131	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477595.1	s__Fabibacter sp002477595	77.1081	52	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	99.68	99.60	0.84	0.83	4	-
GCF_017592825.1	s__Fabibacter sp017592825	77.0652	86	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747095.1	s__Fabibacter sp001747095	77.0019	89	422	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:53,023] [INFO] GTDB search result was written to OceanDNA-b4060/result_gtdb.tsv
[2023-03-18 21:16:53,024] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:53,026] [INFO] DFAST_QC result json was written to OceanDNA-b4060/dqc_result.json
[2023-03-18 21:16:53,026] [INFO] DFAST_QC completed!
[2023-03-18 21:16:53,026] [INFO] Total running time: 0h1m24s