[2023-03-19 02:25:43,937] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:25:43,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:25:43,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference
[2023-03-19 02:25:45,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:25:45,045] [INFO] Task started: Prodigal
[2023-03-19 02:25:45,045] [INFO] Running command: cat /var/lib/cwl/stge40822b4-1e91-458d-b700-0841f712712b/OceanDNA-b29496.fa | prodigal -d OceanDNA-b29496/cds.fna -a OceanDNA-b29496/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:26:07,242] [INFO] Task succeeded: Prodigal
[2023-03-19 02:26:07,243] [INFO] Task started: HMMsearch
[2023-03-19 02:26:07,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b29496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/reference_markers.hmm OceanDNA-b29496/protein.faa > /dev/null
[2023-03-19 02:26:07,462] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:26:07,463] [INFO] Found 6/6 markers.
[2023-03-19 02:26:07,505] [INFO] Query marker FASTA was written to OceanDNA-b29496/markers.fasta
[2023-03-19 02:26:07,507] [INFO] Task started: Blastn
[2023-03-19 02:26:07,507] [INFO] Running command: blastn -query OceanDNA-b29496/markers.fasta -db /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/reference_markers.fasta -out OceanDNA-b29496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:26:08,192] [INFO] Task succeeded: Blastn
[2023-03-19 02:26:08,198] [INFO] Selected 20 target genomes.
[2023-03-19 02:26:08,198] [INFO] Target genome list was writen to OceanDNA-b29496/target_genomes.txt
[2023-03-19 02:26:08,211] [INFO] Task started: fastANI
[2023-03-19 02:26:08,211] [INFO] Running command: fastANI --query /var/lib/cwl/stge40822b4-1e91-458d-b700-0841f712712b/OceanDNA-b29496.fa --refList OceanDNA-b29496/target_genomes.txt --output OceanDNA-b29496/fastani_result.tsv --threads 1
[2023-03-19 02:26:21,822] [INFO] Task succeeded: fastANI
[2023-03-19 02:26:21,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:26:21,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:26:21,834] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 02:26:21,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:26:21,834] [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
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	97.5046	996	1147	95	conclusive
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	80.2883	637	1147	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	79.6773	529	1147	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.7397	336	1147	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.2854	260	1147	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	77.2165	248	1147	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.13	234	1147	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.0188	172	1147	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.0145	197	1147	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.9399	197	1147	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.8951	223	1147	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8653	205	1147	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	76.7844	146	1147	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	76.7517	158	1147	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.7497	203	1147	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.7341	219	1147	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.7008	188	1147	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.6166	178	1147	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.605	183	1147	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	76.3832	164	1147	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:26:21,837] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29496/tc_result.tsv
[2023-03-19 02:26:21,842] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:26:21,842] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:26:21,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/checkm_data
[2023-03-19 02:26:21,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:26:21,899] [INFO] Task started: CheckM
[2023-03-19 02:26:21,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29496/checkm_input OceanDNA-b29496/checkm_result
[2023-03-19 02:27:17,603] [INFO] Task succeeded: CheckM
[2023-03-19 02:27:17,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:27:17,667] [INFO] ===== Completeness check finished =====
[2023-03-19 02:27:17,667] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:27:17,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29496/markers.fasta)
[2023-03-19 02:27:17,668] [INFO] Task started: Blastn
[2023-03-19 02:27:17,668] [INFO] Running command: blastn -query OceanDNA-b29496/markers.fasta -db /var/lib/cwl/stg3edf2a08-5c9e-44fc-a4b2-851f7f9b069d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:27:18,745] [INFO] Task succeeded: Blastn
[2023-03-19 02:27:18,751] [INFO] Selected 11 target genomes.
[2023-03-19 02:27:18,751] [INFO] Target genome list was writen to OceanDNA-b29496/target_genomes_gtdb.txt
[2023-03-19 02:27:18,765] [INFO] Task started: fastANI
[2023-03-19 02:27:18,765] [INFO] Running command: fastANI --query /var/lib/cwl/stge40822b4-1e91-458d-b700-0841f712712b/OceanDNA-b29496.fa --refList OceanDNA-b29496/target_genomes_gtdb.txt --output OceanDNA-b29496/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:27:26,882] [INFO] Task succeeded: fastANI
[2023-03-19 02:27:26,889] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:27:26,889] [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_900114485.1	s__Loktanella salsilacus	97.5275	995	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	conclusive
GCF_900128995.1	s__Loktanella atrilutea	80.2791	638	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	79.6815	528	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	78.7691	444	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	78.685	452	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110705.1	s__Loktanella sp900110705	78.6266	428	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	77.7755	343	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.7288	337	1147	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	77.5498	295	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390475.1	s__Yoonia sp017390475	77.476	284	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	76.3832	164	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:27:26,892] [INFO] GTDB search result was written to OceanDNA-b29496/result_gtdb.tsv
[2023-03-19 02:27:26,901] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:27:26,908] [INFO] DFAST_QC result json was written to OceanDNA-b29496/dqc_result.json
[2023-03-19 02:27:26,908] [INFO] DFAST_QC completed!
[2023-03-19 02:27:26,908] [INFO] Total running time: 0h1m43s