[2023-03-17 22:37:12,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference
[2023-03-17 22:37:14,345] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,346] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,346] [INFO] Running command: cat /var/lib/cwl/stg28db132c-41b5-45b1-9dbf-9302713aa78d/OceanDNA-b3672.fa | prodigal -d OceanDNA-b3672/cds.fna -a OceanDNA-b3672/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:36,643] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:36,643] [INFO] Task started: HMMsearch
[2023-03-17 22:37:36,643] [INFO] Running command: hmmsearch --tblout OceanDNA-b3672/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/reference_markers.hmm OceanDNA-b3672/protein.faa > /dev/null
[2023-03-17 22:37:36,825] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:36,826] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg28db132c-41b5-45b1-9dbf-9302713aa78d/OceanDNA-b3672.fa]
[2023-03-17 22:37:36,846] [INFO] Query marker FASTA was written to OceanDNA-b3672/markers.fasta
[2023-03-17 22:37:36,847] [INFO] Task started: Blastn
[2023-03-17 22:37:36,847] [INFO] Running command: blastn -query OceanDNA-b3672/markers.fasta -db /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/reference_markers.fasta -out OceanDNA-b3672/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:37,417] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:37,418] [INFO] Selected 22 target genomes.
[2023-03-17 22:37:37,418] [INFO] Target genome list was writen to OceanDNA-b3672/target_genomes.txt
[2023-03-17 22:37:37,428] [INFO] Task started: fastANI
[2023-03-17 22:37:37,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg28db132c-41b5-45b1-9dbf-9302713aa78d/OceanDNA-b3672.fa --refList OceanDNA-b3672/target_genomes.txt --output OceanDNA-b3672/fastani_result.tsv --threads 1
[2023-03-17 22:37:53,527] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:53,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:53,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:53,535] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:53,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:37:53,535] [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
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.3977	53	943	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	75.2732	63	943	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.9095	154	943	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	74.8885	80	943	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	74.8089	75	943	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7387	95	943	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.7157	131	943	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	74.7047	58	943	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	74.5759	103	943	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:37:53,535] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3672/tc_result.tsv
[2023-03-17 22:37:53,535] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:53,535] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:53,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/checkm_data
[2023-03-17 22:37:53,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:53,543] [INFO] Task started: CheckM
[2023-03-17 22:37:53,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3672/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3672/checkm_input OceanDNA-b3672/checkm_result
[2023-03-17 22:38:47,920] [INFO] Task succeeded: CheckM
[2023-03-17 22:38:47,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:38:47,923] [INFO] ===== Completeness check finished =====
[2023-03-17 22:38:47,923] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:38:47,923] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3672/markers.fasta)
[2023-03-17 22:38:47,924] [INFO] Task started: Blastn
[2023-03-17 22:38:47,924] [INFO] Running command: blastn -query OceanDNA-b3672/markers.fasta -db /var/lib/cwl/stgfeba6b56-28fb-4983-ac96-9ef2c40566e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3672/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:38:48,787] [INFO] Task succeeded: Blastn
[2023-03-17 22:38:48,788] [INFO] Selected 20 target genomes.
[2023-03-17 22:38:48,788] [INFO] Target genome list was writen to OceanDNA-b3672/target_genomes_gtdb.txt
[2023-03-17 22:38:48,912] [INFO] Task started: fastANI
[2023-03-17 22:38:48,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg28db132c-41b5-45b1-9dbf-9302713aa78d/OceanDNA-b3672.fa --refList OceanDNA-b3672/target_genomes_gtdb.txt --output OceanDNA-b3672/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:39:00,572] [INFO] Task succeeded: fastANI
[2023-03-17 22:39:00,577] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:39:00,577] [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_015490175.1	s__WFYJ01 sp015490175	75.8441	72	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	75.7318	77	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	75.2732	63	943	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	75.136	92	943	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283365.1	s__Rubrivirga marina	74.9089	154	943	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 22:39:00,577] [INFO] GTDB search result was written to OceanDNA-b3672/result_gtdb.tsv
[2023-03-17 22:39:00,577] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:39:00,579] [INFO] DFAST_QC result json was written to OceanDNA-b3672/dqc_result.json
[2023-03-17 22:39:00,579] [INFO] DFAST_QC completed!
[2023-03-17 22:39:00,579] [INFO] Total running time: 0h1m48s