[2023-03-19 03:03:27,564] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:03:27,564] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:03:27,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference
[2023-03-19 03:03:30,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:03:30,631] [INFO] Task started: Prodigal
[2023-03-19 03:03:30,632] [INFO] Running command: cat /var/lib/cwl/stg73c33302-6e31-4d49-bd29-494d534588e8/OceanDNA-b30666.fa | prodigal -d OceanDNA-b30666/cds.fna -a OceanDNA-b30666/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:03:44,494] [INFO] Task succeeded: Prodigal
[2023-03-19 03:03:44,495] [INFO] Task started: HMMsearch
[2023-03-19 03:03:44,495] [INFO] Running command: hmmsearch --tblout OceanDNA-b30666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/reference_markers.hmm OceanDNA-b30666/protein.faa > /dev/null
[2023-03-19 03:03:44,687] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:03:44,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg73c33302-6e31-4d49-bd29-494d534588e8/OceanDNA-b30666.fa]
[2023-03-19 03:03:44,712] [INFO] Query marker FASTA was written to OceanDNA-b30666/markers.fasta
[2023-03-19 03:03:44,714] [INFO] Task started: Blastn
[2023-03-19 03:03:44,714] [INFO] Running command: blastn -query OceanDNA-b30666/markers.fasta -db /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/reference_markers.fasta -out OceanDNA-b30666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:03:45,317] [INFO] Task succeeded: Blastn
[2023-03-19 03:03:45,320] [INFO] Selected 29 target genomes.
[2023-03-19 03:03:45,320] [INFO] Target genome list was writen to OceanDNA-b30666/target_genomes.txt
[2023-03-19 03:03:45,343] [INFO] Task started: fastANI
[2023-03-19 03:03:45,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c33302-6e31-4d49-bd29-494d534588e8/OceanDNA-b30666.fa --refList OceanDNA-b30666/target_genomes.txt --output OceanDNA-b30666/fastani_result.tsv --threads 1
[2023-03-19 03:04:02,064] [INFO] Task succeeded: fastANI
[2023-03-19 03:04:02,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:04:02,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:04:02,087] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:04:02,087] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:04:02,087] [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	77.3715	160	689	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.0828	170	689	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	76.891	149	689	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.79	171	689	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.7155	140	689	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.6988	141	689	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.6701	137	689	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.489	84	689	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.2829	83	689	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.2675	85	689	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.2492	89	689	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.1965	91	689	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	76.1406	100	689	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	76.1221	68	689	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.0542	69	689	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.0059	86	689	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	75.9665	62	689	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	75.8777	72	689	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	75.8499	57	689	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	75.845	65	689	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	75.8287	56	689	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	75.8204	62	689	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	75.7459	66	689	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	75.724	74	689	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	75.6898	69	689	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.4689	55	689	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:04:02,088] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30666/tc_result.tsv
[2023-03-19 03:04:02,088] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:04:02,088] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:04:02,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/checkm_data
[2023-03-19 03:04:02,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:04:02,095] [INFO] Task started: CheckM
[2023-03-19 03:04:02,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30666/checkm_input OceanDNA-b30666/checkm_result
[2023-03-19 03:04:41,416] [INFO] Task succeeded: CheckM
[2023-03-19 03:04:41,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.81%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:04:41,434] [INFO] ===== Completeness check finished =====
[2023-03-19 03:04:41,435] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:04:41,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30666/markers.fasta)
[2023-03-19 03:04:41,436] [INFO] Task started: Blastn
[2023-03-19 03:04:41,436] [INFO] Running command: blastn -query OceanDNA-b30666/markers.fasta -db /var/lib/cwl/stg4a7a2a60-a5ec-4954-a9da-58ff4d78d308/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:04:42,440] [INFO] Task succeeded: Blastn
[2023-03-19 03:04:42,444] [INFO] Selected 18 target genomes.
[2023-03-19 03:04:42,444] [INFO] Target genome list was writen to OceanDNA-b30666/target_genomes_gtdb.txt
[2023-03-19 03:04:42,465] [INFO] Task started: fastANI
[2023-03-19 03:04:42,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c33302-6e31-4d49-bd29-494d534588e8/OceanDNA-b30666.fa --refList OceanDNA-b30666/target_genomes_gtdb.txt --output OceanDNA-b30666/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:04:54,020] [INFO] Task succeeded: fastANI
[2023-03-19 03:04:54,030] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:04:54,030] [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	85.3036	475	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378665.1	s__Yoonia sp002378665	78.0532	238	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	99.59	99.15	0.91	0.87	4	-
GCF_003318235.1	s__Yoonia sp003318235	77.441	136	689	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	77.0828	170	689	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	77.0442	164	689	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	76.79	171	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_003058085.1	s__Yoonia sediminilitoris	76.7155	140	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000169435.1	s__Yoonia sp000169435	76.6857	164	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	76.6701	137	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCA_018402175.1	s__Yoonia sp018402175	76.5786	139	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.5016	133	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	76.4889	103	689	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	76.339	104	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	76.166	93	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_900128995.1	s__Loktanella atrilutea	76.0716	68	689	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	75.8777	72	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	75.8103	57	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313245.1	s__Primorskyibacter marinus	75.7075	68	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:04:54,031] [INFO] GTDB search result was written to OceanDNA-b30666/result_gtdb.tsv
[2023-03-19 03:04:54,032] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:04:54,036] [INFO] DFAST_QC result json was written to OceanDNA-b30666/dqc_result.json
[2023-03-19 03:04:54,036] [INFO] DFAST_QC completed!
[2023-03-19 03:04:54,036] [INFO] Total running time: 0h1m26s