[2023-03-16 07:28:30,013] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,013] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference
[2023-03-16 07:28:31,120] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,121] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,121] [INFO] Running command: cat /var/lib/cwl/stg8d01487e-c46d-447a-be86-0a9e12cfa610/OceanDNA-b30716.fa | prodigal -d OceanDNA-b30716/cds.fna -a OceanDNA-b30716/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:52,794] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:52,794] [INFO] Task started: HMMsearch
[2023-03-16 07:28:52,794] [INFO] Running command: hmmsearch --tblout OceanDNA-b30716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/reference_markers.hmm OceanDNA-b30716/protein.faa > /dev/null
[2023-03-16 07:28:52,983] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:52,984] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8d01487e-c46d-447a-be86-0a9e12cfa610/OceanDNA-b30716.fa]
[2023-03-16 07:28:53,008] [INFO] Query marker FASTA was written to OceanDNA-b30716/markers.fasta
[2023-03-16 07:28:53,009] [INFO] Task started: Blastn
[2023-03-16 07:28:53,009] [INFO] Running command: blastn -query OceanDNA-b30716/markers.fasta -db /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/reference_markers.fasta -out OceanDNA-b30716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:53,604] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:53,605] [INFO] Selected 18 target genomes.
[2023-03-16 07:28:53,605] [INFO] Target genome list was writen to OceanDNA-b30716/target_genomes.txt
[2023-03-16 07:28:53,622] [INFO] Task started: fastANI
[2023-03-16 07:28:53,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d01487e-c46d-447a-be86-0a9e12cfa610/OceanDNA-b30716.fa --refList OceanDNA-b30716/target_genomes.txt --output OceanDNA-b30716/fastani_result.tsv --threads 1
[2023-03-16 07:29:06,576] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:06,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:06,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:06,587] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:06,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:06,587] [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 vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	79.3985	475	1144	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.9106	385	1144	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.8607	338	1144	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.7454	336	1144	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.7091	292	1144	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.6926	364	1144	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.6812	355	1144	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.5764	247	1144	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.4906	330	1144	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.4906	330	1144	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.4073	283	1144	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3876	314	1144	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.384	305	1144	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	77.3633	259	1144	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.3494	323	1144	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.3145	307	1144	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.1963	292	1144	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	77.0538	239	1144	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:06,588] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30716/tc_result.tsv
[2023-03-16 07:29:06,588] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:06,588] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:06,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/checkm_data
[2023-03-16 07:29:06,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:06,622] [INFO] Task started: CheckM
[2023-03-16 07:29:06,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30716/checkm_input OceanDNA-b30716/checkm_result
[2023-03-16 07:30:01,993] [INFO] Task succeeded: CheckM
[2023-03-16 07:30:01,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:30:01,996] [INFO] ===== Completeness check finished =====
[2023-03-16 07:30:01,997] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:30:01,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30716/markers.fasta)
[2023-03-16 07:30:01,998] [INFO] Task started: Blastn
[2023-03-16 07:30:01,998] [INFO] Running command: blastn -query OceanDNA-b30716/markers.fasta -db /var/lib/cwl/stg4687ce23-d7c4-41c4-b35f-bb4965cbdf86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:30:02,859] [INFO] Task succeeded: Blastn
[2023-03-16 07:30:02,860] [INFO] Selected 16 target genomes.
[2023-03-16 07:30:02,860] [INFO] Target genome list was writen to OceanDNA-b30716/target_genomes_gtdb.txt
[2023-03-16 07:30:03,112] [INFO] Task started: fastANI
[2023-03-16 07:30:03,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d01487e-c46d-447a-be86-0a9e12cfa610/OceanDNA-b30716.fa --refList OceanDNA-b30716/target_genomes_gtdb.txt --output OceanDNA-b30716/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:13,968] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:13,978] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:30:13,978] [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_000382265.1	s__Yoonia vestfoldensis	79.388	476	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	79.2272	469	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859355.1	s__Yoonia sp014859355	78.8785	435	1144	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	78.7444	444	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	78.2247	362	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	78.0977	417	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	77.9199	384	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.9143	369	1144	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	77.85	343	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	77.8499	339	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.7733	332	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058085.1	s__Yoonia sediminilitoris	77.4906	330	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011048875.1	s__Rhodovulum sp011048875	77.4608	229	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	77.3338	305	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	77.232	350	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	77.2061	291	1144	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:13,978] [INFO] GTDB search result was written to OceanDNA-b30716/result_gtdb.tsv
[2023-03-16 07:30:13,978] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:13,980] [INFO] DFAST_QC result json was written to OceanDNA-b30716/dqc_result.json
[2023-03-16 07:30:13,980] [INFO] DFAST_QC completed!
[2023-03-16 07:30:13,980] [INFO] Total running time: 0h1m44s