[2023-03-18 20:55:47,242] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,243] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stg7332c534-1d17-4671-8d7e-8828491283d9/OceanDNA-b29553.fa | prodigal -d OceanDNA-b29553/cds.fna -a OceanDNA-b29553/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:55:59,604] [INFO] Task succeeded: Prodigal
[2023-03-18 20:55:59,605] [INFO] Task started: HMMsearch
[2023-03-18 20:55:59,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b29553/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/reference_markers.hmm OceanDNA-b29553/protein.faa > /dev/null
[2023-03-18 20:55:59,745] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:55:59,746] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7332c534-1d17-4671-8d7e-8828491283d9/OceanDNA-b29553.fa]
[2023-03-18 20:55:59,762] [INFO] Query marker FASTA was written to OceanDNA-b29553/markers.fasta
[2023-03-18 20:55:59,762] [INFO] Task started: Blastn
[2023-03-18 20:55:59,763] [INFO] Running command: blastn -query OceanDNA-b29553/markers.fasta -db /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/reference_markers.fasta -out OceanDNA-b29553/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:00,294] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:00,295] [INFO] Selected 10 target genomes.
[2023-03-18 20:56:00,295] [INFO] Target genome list was writen to OceanDNA-b29553/target_genomes.txt
[2023-03-18 20:56:00,300] [INFO] Task started: fastANI
[2023-03-18 20:56:00,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg7332c534-1d17-4671-8d7e-8828491283d9/OceanDNA-b29553.fa --refList OceanDNA-b29553/target_genomes.txt --output OceanDNA-b29553/fastani_result.tsv --threads 1
[2023-03-18 20:56:07,030] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:07,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:07,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:07,038] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:07,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:56:07,038] [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
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	79.1469	359	578	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	79.0177	352	578	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	78.6565	310	578	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8818	215	578	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.7568	225	578	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.5753	199	578	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	77.11	161	578	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	77.0383	165	578	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	76.878	158	578	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	76.5257	144	578	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:56:07,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29553/tc_result.tsv
[2023-03-18 20:56:07,038] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:07,038] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:07,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/checkm_data
[2023-03-18 20:56:07,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:07,042] [INFO] Task started: CheckM
[2023-03-18 20:56:07,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29553/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29553/checkm_input OceanDNA-b29553/checkm_result
[2023-03-18 20:56:38,807] [INFO] Task succeeded: CheckM
[2023-03-18 20:56:38,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:56:38,810] [INFO] ===== Completeness check finished =====
[2023-03-18 20:56:38,810] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:56:38,810] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29553/markers.fasta)
[2023-03-18 20:56:38,810] [INFO] Task started: Blastn
[2023-03-18 20:56:38,810] [INFO] Running command: blastn -query OceanDNA-b29553/markers.fasta -db /var/lib/cwl/stg813e57d7-79ee-4ea0-8257-3abef4e1664d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29553/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:39,542] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:39,543] [INFO] Selected 11 target genomes.
[2023-03-18 20:56:39,543] [INFO] Target genome list was writen to OceanDNA-b29553/target_genomes_gtdb.txt
[2023-03-18 20:56:39,552] [INFO] Task started: fastANI
[2023-03-18 20:56:39,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg7332c534-1d17-4671-8d7e-8828491283d9/OceanDNA-b29553.fa --refList OceanDNA-b29553/target_genomes_gtdb.txt --output OceanDNA-b29553/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:56:46,708] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:46,715] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:56:46,715] [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_013155465.1	s__Alterinioella nitratireducens	82.0065	439	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_004000255.1	s__Nioella ostreopsis	79.1469	359	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	79.0309	351	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001879715.1	s__Nioella nitratireducens	78.6565	310	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	77.8975	214	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	77.8657	244	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.7841	235	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	77.7451	225	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.6203	216	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.4891	203	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	76.878	158	578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:56:46,715] [INFO] GTDB search result was written to OceanDNA-b29553/result_gtdb.tsv
[2023-03-18 20:56:46,715] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:56:46,717] [INFO] DFAST_QC result json was written to OceanDNA-b29553/dqc_result.json
[2023-03-18 20:56:46,717] [INFO] DFAST_QC completed!
[2023-03-18 20:56:46,717] [INFO] Total running time: 0h0m59s