[2024-01-24 13:37:05,184] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,186] [INFO] DQC Reference Directory: /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference
[2024-01-24 13:37:06,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,514] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg2767f0ef-3432-4748-9800-ff2a2b25e8e5/GCF_009762325.1_ASM976232v1_genomic.fna.gz | prodigal -d GCF_009762325.1_ASM976232v1_genomic.fna/cds.fna -a GCF_009762325.1_ASM976232v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:19,709] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:19,709] [INFO] Task started: HMMsearch
[2024-01-24 13:37:19,709] [INFO] Running command: hmmsearch --tblout GCF_009762325.1_ASM976232v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/reference_markers.hmm GCF_009762325.1_ASM976232v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:20,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:20,051] [INFO] Found 6/6 markers.
[2024-01-24 13:37:20,085] [INFO] Query marker FASTA was written to GCF_009762325.1_ASM976232v1_genomic.fna/markers.fasta
[2024-01-24 13:37:20,085] [INFO] Task started: Blastn
[2024-01-24 13:37:20,085] [INFO] Running command: blastn -query GCF_009762325.1_ASM976232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/reference_markers.fasta -out GCF_009762325.1_ASM976232v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:20,872] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:20,877] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:20,878] [INFO] Target genome list was writen to GCF_009762325.1_ASM976232v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:20,885] [INFO] Task started: fastANI
[2024-01-24 13:37:20,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg2767f0ef-3432-4748-9800-ff2a2b25e8e5/GCF_009762325.1_ASM976232v1_genomic.fna.gz --refList GCF_009762325.1_ASM976232v1_genomic.fna/target_genomes.txt --output GCF_009762325.1_ASM976232v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,923] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,941] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:39,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,941] [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
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	100.0	1311	1311	95	conclusive
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.2266	541	1311	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.221	571	1311	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.1721	535	1311	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.161	549	1311	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.1421	548	1311	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.1005	532	1311	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.0887	623	1311	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.0744	623	1311	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	79.0634	624	1311	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	78.6161	508	1311	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.5755	444	1311	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	78.5185	525	1311	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.5029	441	1311	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.1361	416	1311	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	78.0258	439	1311	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.9866	378	1311	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.9323	376	1311	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.8337	367	1311	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.6294	375	1311	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.3736	311	1311	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2675	272	1311	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2656	262	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,942] [INFO] DFAST Taxonomy check result was written to GCF_009762325.1_ASM976232v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/checkm_data
[2024-01-24 13:37:39,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,987] [INFO] Task started: CheckM
[2024-01-24 13:37:39,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009762325.1_ASM976232v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009762325.1_ASM976232v1_genomic.fna/checkm_input GCF_009762325.1_ASM976232v1_genomic.fna/checkm_result
[2024-01-24 13:38:26,896] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:26,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:26,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:26,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:26,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009762325.1_ASM976232v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:26,920] [INFO] Task started: Blastn
[2024-01-24 13:38:26,920] [INFO] Running command: blastn -query GCF_009762325.1_ASM976232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga26cacaa-38e2-43e6-931c-62fa724e5cbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009762325.1_ASM976232v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:28,286] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:28,291] [INFO] Selected 24 target genomes.
[2024-01-24 13:38:28,291] [INFO] Target genome list was writen to GCF_009762325.1_ASM976232v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:28,390] [INFO] Task started: fastANI
[2024-01-24 13:38:28,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg2767f0ef-3432-4748-9800-ff2a2b25e8e5/GCF_009762325.1_ASM976232v1_genomic.fna.gz --refList GCF_009762325.1_ASM976232v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009762325.1_ASM976232v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:46,921] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:46,946] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:46,946] [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_009762325.1	s__Roseovarius faecimaris	100.0	1311	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142765.1	s__Roseovarius litoreus	79.2267	541	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_000152625.1	s__Roseovarius nubinhibens	79.2134	573	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_900109855.1	s__Roseovarius tolerans	79.1755	548	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_900142665.1	s__Roseovarius pacificus	79.1528	550	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_008728195.1	s__Roseovarius indicus	79.0914	622	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_002917925.1	s__Roseovarius confluentis	79.0823	534	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_009363715.1	s__Roseovarius sp009363715	78.9742	537	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	78.9694	417	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	78.9528	519	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172285.1	s__Roseovarius aestuarii	78.6233	503	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761875.1	s__Roseovarius aestuariivivens	78.6106	508	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.598	446	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	78.5846	443	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.5829	501	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125415.1	s__Roseovarius sp007125415	78.5279	396	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.81	0.81	2	-
GCA_900313005.1	s__Roseovarius sp900313005	78.5216	583	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172365.1	s__Roseovarius gaetbuli	78.5185	525	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	78.5033	441	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	78.1544	379	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.0462	377	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172295.1	s__Roseovarius litorisediminis	78.03	439	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.0219	373	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_009789075.1	s__Pseudooceanicola pacificus	77.9553	299	1311	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:46,948] [INFO] GTDB search result was written to GCF_009762325.1_ASM976232v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:46,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:46,953] [INFO] DFAST_QC result json was written to GCF_009762325.1_ASM976232v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:46,954] [INFO] DFAST_QC completed!
[2024-01-24 13:38:46,954] [INFO] Total running time: 0h1m42s