[2023-03-19 04:11:06,923] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg7c5ac452-4126-495f-aaea-7bb0312bb3aa/OceanDNA-b30647.fa | prodigal -d OceanDNA-b30647/cds.fna -a OceanDNA-b30647/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:23,016] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:23,016] [INFO] Task started: HMMsearch
[2023-03-19 04:11:23,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b30647/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/reference_markers.hmm OceanDNA-b30647/protein.faa > /dev/null
[2023-03-19 04:11:23,195] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:23,196] [INFO] Found 6/6 markers.
[2023-03-19 04:11:23,213] [INFO] Query marker FASTA was written to OceanDNA-b30647/markers.fasta
[2023-03-19 04:11:23,213] [INFO] Task started: Blastn
[2023-03-19 04:11:23,213] [INFO] Running command: blastn -query OceanDNA-b30647/markers.fasta -db /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/reference_markers.fasta -out OceanDNA-b30647/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:23,789] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:23,790] [INFO] Selected 28 target genomes.
[2023-03-19 04:11:23,790] [INFO] Target genome list was writen to OceanDNA-b30647/target_genomes.txt
[2023-03-19 04:11:23,804] [INFO] Task started: fastANI
[2023-03-19 04:11:23,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5ac452-4126-495f-aaea-7bb0312bb3aa/OceanDNA-b30647.fa --refList OceanDNA-b30647/target_genomes.txt --output OceanDNA-b30647/fastani_result.tsv --threads 1
[2023-03-19 04:11:40,293] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:40,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:40,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:40,306] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:40,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:40,306] [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
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	77.8505	169	738	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.7117	188	738	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.5276	204	738	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.4146	162	738	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	77.2638	98	738	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.0427	154	738	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.8947	147	738	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.6218	83	738	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.5639	126	738	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.4316	92	738	95	below_threshold
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	76.4122	83	738	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.309	94	738	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.2598	77	738	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.2128	77	738	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	76.1757	84	738	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.0729	77	738	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.071	68	738	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.0112	60	738	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.0054	75	738	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	75.8821	61	738	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	75.8626	64	738	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.7952	67	738	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	75.7132	61	738	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.4012	56	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:40,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30647/tc_result.tsv
[2023-03-19 04:11:40,307] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:40,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:40,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/checkm_data
[2023-03-19 04:11:40,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:40,311] [INFO] Task started: CheckM
[2023-03-19 04:11:40,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30647/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30647/checkm_input OceanDNA-b30647/checkm_result
[2023-03-19 04:12:19,637] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:19,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:19,640] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:19,640] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:19,640] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30647/markers.fasta)
[2023-03-19 04:12:19,640] [INFO] Task started: Blastn
[2023-03-19 04:12:19,640] [INFO] Running command: blastn -query OceanDNA-b30647/markers.fasta -db /var/lib/cwl/stgd256ea6f-5eb9-48da-8e34-b6bcaef1e980/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30647/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:20,502] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:20,503] [INFO] Selected 20 target genomes.
[2023-03-19 04:12:20,503] [INFO] Target genome list was writen to OceanDNA-b30647/target_genomes_gtdb.txt
[2023-03-19 04:12:20,618] [INFO] Task started: fastANI
[2023-03-19 04:12:20,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5ac452-4126-495f-aaea-7bb0312bb3aa/OceanDNA-b30647.fa --refList OceanDNA-b30647/target_genomes_gtdb.txt --output OceanDNA-b30647/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:33,344] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:33,356] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:12:33,356] [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
GCA_905182645.1	s__Yoonia sp905182645	99.2773	640	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002378665.1	s__Yoonia sp002378665	78.3957	270	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCA_017854415.1	s__Yoonia sp017854415	78.0185	186	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199395.1	s__Yoonia ponticola	77.5276	204	738	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	77.4235	158	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.4146	162	738	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	77.2357	177	738	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	77.1399	174	738	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	77.0427	154	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCA_003551805.1	s__Yoonia sp003551805	77.0368	129	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCA_017854565.1	s__Yoonia sp017854565	76.9666	169	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.9025	149	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_900114485.1	s__Loktanella salsilacus	76.8947	147	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.5811	125	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859355.1	s__Yoonia sp014859355	76.4991	150	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	76.3488	110	738	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	76.2128	77	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015220045.1	s__Marivivens aquimaris	76.0112	60	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	76.0054	75	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	75.6557	55	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:33,356] [INFO] GTDB search result was written to OceanDNA-b30647/result_gtdb.tsv
[2023-03-19 04:12:33,356] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:33,358] [INFO] DFAST_QC result json was written to OceanDNA-b30647/dqc_result.json
[2023-03-19 04:12:33,359] [INFO] DFAST_QC completed!
[2023-03-19 04:12:33,359] [INFO] Total running time: 0h1m26s