[2023-03-15 10:56:32,965] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:56:32,966] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:56:32,966] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference
[2023-03-15 10:56:34,092] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:56:34,092] [INFO] Task started: Prodigal
[2023-03-15 10:56:34,092] [INFO] Running command: cat /var/lib/cwl/stgc839c044-a81f-4ea9-af20-c44c4f769728/OceanDNA-b30718.fa | prodigal -d OceanDNA-b30718/cds.fna -a OceanDNA-b30718/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:56:50,966] [INFO] Task succeeded: Prodigal
[2023-03-15 10:56:50,967] [INFO] Task started: HMMsearch
[2023-03-15 10:56:50,967] [INFO] Running command: hmmsearch --tblout OceanDNA-b30718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/reference_markers.hmm OceanDNA-b30718/protein.faa > /dev/null
[2023-03-15 10:56:51,127] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:56:51,128] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc839c044-a81f-4ea9-af20-c44c4f769728/OceanDNA-b30718.fa]
[2023-03-15 10:56:51,147] [INFO] Query marker FASTA was written to OceanDNA-b30718/markers.fasta
[2023-03-15 10:56:51,147] [INFO] Task started: Blastn
[2023-03-15 10:56:51,147] [INFO] Running command: blastn -query OceanDNA-b30718/markers.fasta -db /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/reference_markers.fasta -out OceanDNA-b30718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:56:51,648] [INFO] Task succeeded: Blastn
[2023-03-15 10:56:51,649] [INFO] Selected 14 target genomes.
[2023-03-15 10:56:51,649] [INFO] Target genome list was writen to OceanDNA-b30718/target_genomes.txt
[2023-03-15 10:56:51,656] [INFO] Task started: fastANI
[2023-03-15 10:56:51,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgc839c044-a81f-4ea9-af20-c44c4f769728/OceanDNA-b30718.fa --refList OceanDNA-b30718/target_genomes.txt --output OceanDNA-b30718/fastani_result.tsv --threads 1
[2023-03-15 10:57:00,293] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:00,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:57:00,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:57:00,302] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:57:00,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:57:00,302] [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	79.1645	373	896	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.9741	314	896	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.9554	281	896	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	77.7173	279	896	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	77.7173	279	896	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.4676	252	896	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.4291	242	896	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.2129	209	896	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0761	221	896	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.0062	235	896	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.9285	230	896	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	76.6825	174	896	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	76.6707	172	896	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.6401	136	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:57:00,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30718/tc_result.tsv
[2023-03-15 10:57:00,303] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:57:00,303] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:57:00,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/checkm_data
[2023-03-15 10:57:00,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:57:00,308] [INFO] Task started: CheckM
[2023-03-15 10:57:00,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30718/checkm_input OceanDNA-b30718/checkm_result
[2023-03-15 10:57:44,413] [INFO] Task succeeded: CheckM
[2023-03-15 10:57:44,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.21%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:57:44,416] [INFO] ===== Completeness check finished =====
[2023-03-15 10:57:44,416] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:57:44,416] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30718/markers.fasta)
[2023-03-15 10:57:44,416] [INFO] Task started: Blastn
[2023-03-15 10:57:44,416] [INFO] Running command: blastn -query OceanDNA-b30718/markers.fasta -db /var/lib/cwl/stgcf6c653e-5a9d-460e-9f2b-98251a923d49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:57:45,002] [INFO] Task succeeded: Blastn
[2023-03-15 10:57:45,003] [INFO] Selected 14 target genomes.
[2023-03-15 10:57:45,003] [INFO] Target genome list was writen to OceanDNA-b30718/target_genomes_gtdb.txt
[2023-03-15 10:57:45,013] [INFO] Task started: fastANI
[2023-03-15 10:57:45,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgc839c044-a81f-4ea9-af20-c44c4f769728/OceanDNA-b30718.fa --refList OceanDNA-b30718/target_genomes_gtdb.txt --output OceanDNA-b30718/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:57:54,264] [INFO] Task succeeded: fastANI
[2023-03-15 10:57:54,272] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:57:54,272] [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	79.1654	373	896	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	78.8885	358	896	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	78.8114	355	896	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	78.4665	346	896	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	78.3795	327	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551805.1	s__Yoonia sp003551805	78.2757	260	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCF_003201935.1	s__Yoonia sp003201935	77.8963	291	896	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	77.7214	278	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900143545.1	s__Yoonia sp900143545	77.6444	246	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.3261	260	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	77.2607	244	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	77.2129	209	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.9285	230	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	76.8017	178	896	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:57:54,272] [INFO] GTDB search result was written to OceanDNA-b30718/result_gtdb.tsv
[2023-03-15 10:57:54,273] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:57:54,274] [INFO] DFAST_QC result json was written to OceanDNA-b30718/dqc_result.json
[2023-03-15 10:57:54,274] [INFO] DFAST_QC completed!
[2023-03-15 10:57:54,274] [INFO] Total running time: 0h1m21s