[2023-03-17 03:11:36,313] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,313] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference
[2023-03-17 03:11:37,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,549] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,549] [INFO] Running command: cat /var/lib/cwl/stg895d4e63-02ed-4c33-bd69-f07b1f57d203/OceanDNA-b34219.fa | prodigal -d OceanDNA-b34219/cds.fna -a OceanDNA-b34219/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:12:05,990] [INFO] Task succeeded: Prodigal
[2023-03-17 03:12:05,990] [INFO] Task started: HMMsearch
[2023-03-17 03:12:05,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b34219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/reference_markers.hmm OceanDNA-b34219/protein.faa > /dev/null
[2023-03-17 03:12:06,259] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:12:06,260] [INFO] Found 6/6 markers.
[2023-03-17 03:12:06,291] [INFO] Query marker FASTA was written to OceanDNA-b34219/markers.fasta
[2023-03-17 03:12:06,293] [INFO] Task started: Blastn
[2023-03-17 03:12:06,293] [INFO] Running command: blastn -query OceanDNA-b34219/markers.fasta -db /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/reference_markers.fasta -out OceanDNA-b34219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:06,965] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:06,966] [INFO] Selected 35 target genomes.
[2023-03-17 03:12:06,966] [INFO] Target genome list was writen to OceanDNA-b34219/target_genomes.txt
[2023-03-17 03:12:07,038] [INFO] Task started: fastANI
[2023-03-17 03:12:07,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg895d4e63-02ed-4c33-bd69-f07b1f57d203/OceanDNA-b34219.fa --refList OceanDNA-b34219/target_genomes.txt --output OceanDNA-b34219/fastani_result.tsv --threads 1
[2023-03-17 03:12:33,637] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:33,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:33,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:33,644] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:33,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:33,644] [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
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	75.8618	56	1468	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	75.4882	51	1468	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	75.2979	53	1468	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	75.1508	70	1468	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	75.0887	52	1468	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	75.0789	78	1468	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	75.0357	72	1468	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	74.9655	50	1468	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	74.9347	50	1468	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:33,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34219/tc_result.tsv
[2023-03-17 03:12:33,644] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:33,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:33,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/checkm_data
[2023-03-17 03:12:33,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:33,656] [INFO] Task started: CheckM
[2023-03-17 03:12:33,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34219/checkm_input OceanDNA-b34219/checkm_result
[2023-03-17 03:13:42,536] [INFO] Task succeeded: CheckM
[2023-03-17 03:13:42,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:13:42,540] [INFO] ===== Completeness check finished =====
[2023-03-17 03:13:42,540] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:13:42,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34219/markers.fasta)
[2023-03-17 03:13:42,541] [INFO] Task started: Blastn
[2023-03-17 03:13:42,541] [INFO] Running command: blastn -query OceanDNA-b34219/markers.fasta -db /var/lib/cwl/stg8c04bda1-2719-4379-a52d-eddddd8630ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:13:43,682] [INFO] Task succeeded: Blastn
[2023-03-17 03:13:43,683] [INFO] Selected 17 target genomes.
[2023-03-17 03:13:43,683] [INFO] Target genome list was writen to OceanDNA-b34219/target_genomes_gtdb.txt
[2023-03-17 03:13:43,924] [INFO] Task started: fastANI
[2023-03-17 03:13:43,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg895d4e63-02ed-4c33-bd69-f07b1f57d203/OceanDNA-b34219.fa --refList OceanDNA-b34219/target_genomes_gtdb.txt --output OceanDNA-b34219/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:13:57,691] [INFO] Task succeeded: fastANI
[2023-03-17 03:13:57,699] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:13:57,699] [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_009885185.1	s__UBA5216 sp009885185	77.7419	369	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412495.1	s__UBA5216 sp002412495	77.7219	508	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	99.91	99.91	0.93	0.93	2	-
GCA_902825845.1	s__UBA5216 sp902825845	77.6252	508	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299145.1	s__UBA5216 sp900299145	77.2382	462	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868015.1	s__UBA5216 sp016868015	77.0509	369	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005800795.1	s__UBA5216 sp005800795	76.9526	279	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__UBA5216	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933915.1	s__Ga0077527 sp903933915	76.2838	169	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__Ga0077527	95.0	99.39	99.32	0.93	0.92	3	-
GCA_001464815.1	s__Ga0077527 sp001464815	75.9917	153	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__Ga0077527	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913965.1	s__PALSA-1004 sp903913965	75.8079	103	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	98.84	98.17	0.81	0.70	5	-
GCA_001771985.1	s__DSOT01 sp001771985	75.4285	110	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001580565.1	s__Caballeronia megalochromosomata	75.1654	54	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	75.0771	64	1468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:13:57,699] [INFO] GTDB search result was written to OceanDNA-b34219/result_gtdb.tsv
[2023-03-17 03:13:57,699] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:13:57,700] [INFO] DFAST_QC result json was written to OceanDNA-b34219/dqc_result.json
[2023-03-17 03:13:57,701] [INFO] DFAST_QC completed!
[2023-03-17 03:13:57,701] [INFO] Total running time: 0h2m21s