[2023-03-18 23:44:06,344] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,345] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference
[2023-03-18 23:44:07,452] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,452] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,453] [INFO] Running command: cat /var/lib/cwl/stg033703bc-1a69-4d05-a256-07320ccd801b/OceanDNA-b30724.fa | prodigal -d OceanDNA-b30724/cds.fna -a OceanDNA-b30724/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:23,095] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:23,096] [INFO] Task started: HMMsearch
[2023-03-18 23:44:23,096] [INFO] Running command: hmmsearch --tblout OceanDNA-b30724/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/reference_markers.hmm OceanDNA-b30724/protein.faa > /dev/null
[2023-03-18 23:44:23,271] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:23,272] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg033703bc-1a69-4d05-a256-07320ccd801b/OceanDNA-b30724.fa]
[2023-03-18 23:44:23,292] [INFO] Query marker FASTA was written to OceanDNA-b30724/markers.fasta
[2023-03-18 23:44:23,293] [INFO] Task started: Blastn
[2023-03-18 23:44:23,293] [INFO] Running command: blastn -query OceanDNA-b30724/markers.fasta -db /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/reference_markers.fasta -out OceanDNA-b30724/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:23,764] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:23,764] [INFO] Selected 14 target genomes.
[2023-03-18 23:44:23,765] [INFO] Target genome list was writen to OceanDNA-b30724/target_genomes.txt
[2023-03-18 23:44:23,774] [INFO] Task started: fastANI
[2023-03-18 23:44:23,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg033703bc-1a69-4d05-a256-07320ccd801b/OceanDNA-b30724.fa --refList OceanDNA-b30724/target_genomes.txt --output OceanDNA-b30724/fastani_result.tsv --threads 1
[2023-03-18 23:44:31,857] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:31,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:31,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:31,866] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:31,866] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:31,866] [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
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	79.2991	365	776	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	79.1098	355	776	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.7964	147	776	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.0919	205	776	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.9683	205	776	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.8659	116	776	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.7242	125	776	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.3489	60	776	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	75.8797	54	776	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	75.8544	55	776	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	75.7593	88	776	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	75.6272	51	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:31,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30724/tc_result.tsv
[2023-03-18 23:44:31,866] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:31,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:31,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/checkm_data
[2023-03-18 23:44:31,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:31,881] [INFO] Task started: CheckM
[2023-03-18 23:44:31,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30724/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30724/checkm_input OceanDNA-b30724/checkm_result
[2023-03-18 23:45:13,234] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:13,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:13,243] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:13,243] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:13,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30724/markers.fasta)
[2023-03-18 23:45:13,244] [INFO] Task started: Blastn
[2023-03-18 23:45:13,244] [INFO] Running command: blastn -query OceanDNA-b30724/markers.fasta -db /var/lib/cwl/stg6eb94a00-1ab8-46f3-99ac-c4960a650bae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30724/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:13,752] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:13,755] [INFO] Selected 10 target genomes.
[2023-03-18 23:45:13,756] [INFO] Target genome list was writen to OceanDNA-b30724/target_genomes_gtdb.txt
[2023-03-18 23:45:13,763] [INFO] Task started: fastANI
[2023-03-18 23:45:13,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg033703bc-1a69-4d05-a256-07320ccd801b/OceanDNA-b30724.fa --refList OceanDNA-b30724/target_genomes_gtdb.txt --output OceanDNA-b30724/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:20,226] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:20,232] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:45:20,232] [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_000169435.1	s__Yoonia sp000169435	79.7651	380	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797915.1	s__Yoonia maricola	79.2991	365	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	79.1098	355	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_003201935.1	s__Yoonia sp003201935	79.0951	366	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	79.0746	371	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	78.5378	302	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	76.8683	175	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533975.1	s__Octadecabacter sp003533975	75.815	60	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466965.1	s__Limimaricola cinnabarinus	75.6084	52	776	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:20,234] [INFO] GTDB search result was written to OceanDNA-b30724/result_gtdb.tsv
[2023-03-18 23:45:20,235] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:20,240] [INFO] DFAST_QC result json was written to OceanDNA-b30724/dqc_result.json
[2023-03-18 23:45:20,240] [INFO] DFAST_QC completed!
[2023-03-18 23:45:20,240] [INFO] Total running time: 0h1m14s