[2024-01-24 13:12:48,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:48,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:48,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference
[2024-01-24 13:12:49,398] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:49,399] [INFO] Task started: Prodigal
[2024-01-24 13:12:49,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa8fdcda-afb7-4e82-a99b-a2f54006c18c/GCF_014199615.1_ASM1419961v1_genomic.fna.gz | prodigal -d GCF_014199615.1_ASM1419961v1_genomic.fna/cds.fna -a GCF_014199615.1_ASM1419961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:57,304] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:57,304] [INFO] Task started: HMMsearch
[2024-01-24 13:12:57,304] [INFO] Running command: hmmsearch --tblout GCF_014199615.1_ASM1419961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/reference_markers.hmm GCF_014199615.1_ASM1419961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:57,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:57,603] [INFO] Found 6/6 markers.
[2024-01-24 13:12:57,634] [INFO] Query marker FASTA was written to GCF_014199615.1_ASM1419961v1_genomic.fna/markers.fasta
[2024-01-24 13:12:57,635] [INFO] Task started: Blastn
[2024-01-24 13:12:57,635] [INFO] Running command: blastn -query GCF_014199615.1_ASM1419961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/reference_markers.fasta -out GCF_014199615.1_ASM1419961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:58,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:58,643] [INFO] Selected 17 target genomes.
[2024-01-24 13:12:58,643] [INFO] Target genome list was writen to GCF_014199615.1_ASM1419961v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:58,687] [INFO] Task started: fastANI
[2024-01-24 13:12:58,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8fdcda-afb7-4e82-a99b-a2f54006c18c/GCF_014199615.1_ASM1419961v1_genomic.fna.gz --refList GCF_014199615.1_ASM1419961v1_genomic.fna/target_genomes.txt --output GCF_014199615.1_ASM1419961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:13,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:13,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:13,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:13,021] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:13,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:13,021] [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
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	100.0	1037	1039	95	conclusive
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	80.3675	528	1039	95	below_threshold
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	77.7746	238	1039	95	below_threshold
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	77.6362	204	1039	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	77.4577	152	1039	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	77.427	153	1039	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.2273	166	1039	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.1818	168	1039	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	77.1752	137	1039	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.73	178	1039	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.5908	162	1039	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	76.4895	202	1039	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4113	181	1039	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	76.2887	195	1039	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	76.2767	157	1039	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.239	240	1039	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.1862	157	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:13,023] [INFO] DFAST Taxonomy check result was written to GCF_014199615.1_ASM1419961v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:13,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:13,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:13,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/checkm_data
[2024-01-24 13:13:13,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:13,062] [INFO] Task started: CheckM
[2024-01-24 13:13:13,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199615.1_ASM1419961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199615.1_ASM1419961v1_genomic.fna/checkm_input GCF_014199615.1_ASM1419961v1_genomic.fna/checkm_result
[2024-01-24 13:13:41,312] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:41,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:41,340] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:41,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:41,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199615.1_ASM1419961v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:41,342] [INFO] Task started: Blastn
[2024-01-24 13:13:41,342] [INFO] Running command: blastn -query GCF_014199615.1_ASM1419961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c947a4-5de0-4de9-b36f-7d5c23bc3ff3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199615.1_ASM1419961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:43,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:43,113] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:43,113] [INFO] Target genome list was writen to GCF_014199615.1_ASM1419961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:43,126] [INFO] Task started: fastANI
[2024-01-24 13:13:43,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8fdcda-afb7-4e82-a99b-a2f54006c18c/GCF_014199615.1_ASM1419961v1_genomic.fna.gz --refList GCF_014199615.1_ASM1419961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199615.1_ASM1419961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:54,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:54,146] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:54,146] [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_014199615.1	s__Parvularcula dongshanensis	100.0	1037	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000733125.1	s__Parvularcula oceani	80.3516	529	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085255.1	s__Parvularcula mediterranea	77.7887	237	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651915.1	s__Parvularcula lutaonensis	77.6362	204	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	77.4577	152	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640095.1	s__Aquisalinus flavus	77.1981	167	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003399445.1	s__Parvularcula sp003399445	77.1752	137	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122085.1	s__WD6-1 sp003122085	76.7666	175	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	76.7665	168	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	76.5277	238	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043895.1	s__Methylobacterium indicum	76.5087	200	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.73	98.07	0.88	0.87	6	-
GCF_002742635.1	s__Caulobacter sp002742635	76.399	163	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.3371	123	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	76.3082	185	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	75.808	185	1039	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,148] [INFO] GTDB search result was written to GCF_014199615.1_ASM1419961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:54,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:54,152] [INFO] DFAST_QC result json was written to GCF_014199615.1_ASM1419961v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:54,152] [INFO] DFAST_QC completed!
[2024-01-24 13:13:54,152] [INFO] Total running time: 0h1m6s