[2023-06-30 04:32:53,244] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:32:53,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:32:53,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference
[2023-06-30 04:32:54,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:32:54,889] [INFO] Task started: Prodigal
[2023-06-30 04:32:54,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea51cd8-2dad-4893-9b61-cffc5b7d5fe6/GCA_024686115.1_ASM2468611v1_genomic.fna.gz | prodigal -d GCA_024686115.1_ASM2468611v1_genomic.fna/cds.fna -a GCA_024686115.1_ASM2468611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:33:05,167] [INFO] Task succeeded: Prodigal
[2023-06-30 04:33:05,168] [INFO] Task started: HMMsearch
[2023-06-30 04:33:05,168] [INFO] Running command: hmmsearch --tblout GCA_024686115.1_ASM2468611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/reference_markers.hmm GCA_024686115.1_ASM2468611v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:33:05,444] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:33:05,446] [INFO] Found 6/6 markers.
[2023-06-30 04:33:05,482] [INFO] Query marker FASTA was written to GCA_024686115.1_ASM2468611v1_genomic.fna/markers.fasta
[2023-06-30 04:33:05,483] [INFO] Task started: Blastn
[2023-06-30 04:33:05,483] [INFO] Running command: blastn -query GCA_024686115.1_ASM2468611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/reference_markers.fasta -out GCA_024686115.1_ASM2468611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:33:06,180] [INFO] Task succeeded: Blastn
[2023-06-30 04:33:06,187] [INFO] Selected 31 target genomes.
[2023-06-30 04:33:06,188] [INFO] Target genome list was writen to GCA_024686115.1_ASM2468611v1_genomic.fna/target_genomes.txt
[2023-06-30 04:33:06,190] [INFO] Task started: fastANI
[2023-06-30 04:33:06,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea51cd8-2dad-4893-9b61-cffc5b7d5fe6/GCA_024686115.1_ASM2468611v1_genomic.fna.gz --refList GCA_024686115.1_ASM2468611v1_genomic.fna/target_genomes.txt --output GCA_024686115.1_ASM2468611v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:33:26,494] [INFO] Task succeeded: fastANI
[2023-06-30 04:33:26,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:33:26,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:33:26,524] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:33:26,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:33:26,524] [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	77.4834	234	981	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.4133	195	981	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	77.3553	248	981	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.0081	184	981	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.9264	235	981	95	below_threshold
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	76.8304	205	981	95	below_threshold
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	76.8304	205	981	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	76.8188	190	981	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.6562	146	981	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6157	113	981	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	76.5829	174	981	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.4823	81	981	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.4743	120	981	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.4424	130	981	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	76.4156	159	981	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.4123	133	981	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.3549	121	981	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	76.3211	148	981	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.2698	82	981	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.2315	81	981	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.2233	126	981	95	below_threshold
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	76.1892	125	981	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.0606	110	981	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.0315	73	981	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	76.0223	102	981	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	75.9972	87	981	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	75.9799	100	981	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	75.7465	93	981	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.6219	53	981	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:33:26,530] [INFO] DFAST Taxonomy check result was written to GCA_024686115.1_ASM2468611v1_genomic.fna/tc_result.tsv
[2023-06-30 04:33:26,530] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:33:26,530] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:33:26,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/checkm_data
[2023-06-30 04:33:26,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:33:26,576] [INFO] Task started: CheckM
[2023-06-30 04:33:26,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024686115.1_ASM2468611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024686115.1_ASM2468611v1_genomic.fna/checkm_input GCA_024686115.1_ASM2468611v1_genomic.fna/checkm_result
[2023-06-30 04:34:00,829] [INFO] Task succeeded: CheckM
[2023-06-30 04:34:00,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:34:00,858] [INFO] ===== Completeness check finished =====
[2023-06-30 04:34:00,859] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:34:00,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024686115.1_ASM2468611v1_genomic.fna/markers.fasta)
[2023-06-30 04:34:00,860] [INFO] Task started: Blastn
[2023-06-30 04:34:00,860] [INFO] Running command: blastn -query GCA_024686115.1_ASM2468611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca198745-25b7-4322-b022-cadc7c910849/dqc_reference/reference_markers_gtdb.fasta -out GCA_024686115.1_ASM2468611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:34:01,717] [INFO] Task succeeded: Blastn
[2023-06-30 04:34:01,722] [INFO] Selected 20 target genomes.
[2023-06-30 04:34:01,723] [INFO] Target genome list was writen to GCA_024686115.1_ASM2468611v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:34:01,726] [INFO] Task started: fastANI
[2023-06-30 04:34:01,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea51cd8-2dad-4893-9b61-cffc5b7d5fe6/GCA_024686115.1_ASM2468611v1_genomic.fna.gz --refList GCA_024686115.1_ASM2468611v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024686115.1_ASM2468611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:34:13,667] [INFO] Task succeeded: fastANI
[2023-06-30 04:34:13,687] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 04:34:13,688] [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	85.3927	662	981	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	78.2066	342	981	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	77.7139	218	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318235.1	s__Yoonia sp003318235	77.4694	202	981	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	77.4577	182	981	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	77.3553	248	981	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	77.1047	225	981	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	77.0229	215	981	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	76.9264	235	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCF_900114485.1	s__Loktanella salsilacus	76.8317	188	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_003058085.1	s__Yoonia sediminilitoris	76.8304	205	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017854565.1	s__Yoonia sp017854565	76.8076	236	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	76.7285	153	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.6541	191	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	76.5703	113	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109295.1	s__Cognatiyoonia koreensis	76.4133	157	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatiyoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.4123	133	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_001420005.1	s__Loktanella sp001420005	76.331	153	981	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	76.0743	109	981	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	75.7991	86	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:34:13,690] [INFO] GTDB search result was written to GCA_024686115.1_ASM2468611v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:34:13,690] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:34:13,696] [INFO] DFAST_QC result json was written to GCA_024686115.1_ASM2468611v1_genomic.fna/dqc_result.json
[2023-06-30 04:34:13,696] [INFO] DFAST_QC completed!
[2023-06-30 04:34:13,696] [INFO] Total running time: 0h1m20s