[2023-03-15 07:52:40,394] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,394] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,394] [INFO] DQC Reference Directory: /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference
[2023-03-15 07:52:41,610] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,611] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,611] [INFO] Running command: cat /var/lib/cwl/stg75f10aec-ed74-47e7-95f0-35c0d7094127/OceanDNA-b30721.fa | prodigal -d OceanDNA-b30721/cds.fna -a OceanDNA-b30721/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:52,448] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:52,448] [INFO] Task started: HMMsearch
[2023-03-15 07:52:52,449] [INFO] Running command: hmmsearch --tblout OceanDNA-b30721/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/reference_markers.hmm OceanDNA-b30721/protein.faa > /dev/null
[2023-03-15 07:52:52,694] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:52,694] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg75f10aec-ed74-47e7-95f0-35c0d7094127/OceanDNA-b30721.fa]
[2023-03-15 07:52:52,712] [INFO] Query marker FASTA was written to OceanDNA-b30721/markers.fasta
[2023-03-15 07:52:52,712] [INFO] Task started: Blastn
[2023-03-15 07:52:52,712] [INFO] Running command: blastn -query OceanDNA-b30721/markers.fasta -db /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/reference_markers.fasta -out OceanDNA-b30721/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:53,262] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:53,262] [INFO] Selected 19 target genomes.
[2023-03-15 07:52:53,263] [INFO] Target genome list was writen to OceanDNA-b30721/target_genomes.txt
[2023-03-15 07:52:53,273] [INFO] Task started: fastANI
[2023-03-15 07:52:53,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg75f10aec-ed74-47e7-95f0-35c0d7094127/OceanDNA-b30721.fa --refList OceanDNA-b30721/target_genomes.txt --output OceanDNA-b30721/fastani_result.tsv --threads 1
[2023-03-15 07:53:06,748] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:06,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:06,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:06,756] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:06,756] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:06,756] [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 tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	78.7408	223	454	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	78.3414	219	454	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.5894	136	454	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.8285	124	454	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.8285	124	454	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	76.7908	124	454	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.6618	65	454	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.59	91	454	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.5223	64	454	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.3007	61	454	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.5776	51	454	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:06,756] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30721/tc_result.tsv
[2023-03-15 07:53:06,756] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:06,756] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:06,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/checkm_data
[2023-03-15 07:53:06,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:06,761] [INFO] Task started: CheckM
[2023-03-15 07:53:06,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30721/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30721/checkm_input OceanDNA-b30721/checkm_result
[2023-03-15 07:53:38,719] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:38,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:38,722] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:38,722] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:38,722] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30721/markers.fasta)
[2023-03-15 07:53:38,722] [INFO] Task started: Blastn
[2023-03-15 07:53:38,722] [INFO] Running command: blastn -query OceanDNA-b30721/markers.fasta -db /var/lib/cwl/stgd034b67f-4bcb-4835-9c9c-683082bd428c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30721/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:39,552] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:39,553] [INFO] Selected 17 target genomes.
[2023-03-15 07:53:39,553] [INFO] Target genome list was writen to OceanDNA-b30721/target_genomes_gtdb.txt
[2023-03-15 07:53:39,565] [INFO] Task started: fastANI
[2023-03-15 07:53:39,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg75f10aec-ed74-47e7-95f0-35c0d7094127/OceanDNA-b30721.fa --refList OceanDNA-b30721/target_genomes_gtdb.txt --output OceanDNA-b30721/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:50,168] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:50,177] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:50,177] [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_900115105.1	s__Yoonia tamlensis	78.7408	223	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933395.1	s__Yoonia maritima_A	78.5926	214	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	77.7545	156	454	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	77.5894	136	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCA_017390475.1	s__Yoonia sp017390475	77.3434	134	454	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	77.3268	150	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	77.272	135	454	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	77.1619	134	454	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	77.0382	146	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169435.1	s__Yoonia sp000169435	76.8715	129	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058085.1	s__Yoonia sediminilitoris	76.8285	124	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002797915.1	s__Yoonia maricola	76.7908	124	454	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	76.5816	123	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	75.9826	53	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002452815.1	s__UBA6796 sp002452815	75.8551	54	454	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:50,177] [INFO] GTDB search result was written to OceanDNA-b30721/result_gtdb.tsv
[2023-03-15 07:53:50,177] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:50,179] [INFO] DFAST_QC result json was written to OceanDNA-b30721/dqc_result.json
[2023-03-15 07:53:50,179] [INFO] DFAST_QC completed!
[2023-03-15 07:53:50,179] [INFO] Total running time: 0h1m10s