[2024-01-24 12:40:07,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference
[2024-01-24 12:40:08,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,388] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9806faf-a352-403d-a7d6-943062839abe/GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna.gz | prodigal -d GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/cds.fna -a GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:21,399] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:21,399] [INFO] Task started: HMMsearch
[2024-01-24 12:40:21,399] [INFO] Running command: hmmsearch --tblout GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/reference_markers.hmm GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:21,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:21,641] [INFO] Found 6/6 markers.
[2024-01-24 12:40:21,676] [INFO] Query marker FASTA was written to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:40:21,677] [INFO] Task started: Blastn
[2024-01-24 12:40:21,677] [INFO] Running command: blastn -query GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/reference_markers.fasta -out GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:22,391] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:22,394] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:22,395] [INFO] Target genome list was writen to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:40:22,400] [INFO] Task started: fastANI
[2024-01-24 12:40:22,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9806faf-a352-403d-a7d6-943062839abe/GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna.gz --refList GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/target_genomes.txt --output GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:34,312] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:34,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:34,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:34,325] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:34,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:34,326] [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
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	100.0	1309	1314	95	conclusive
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	99.9896	1309	1314	95	conclusive
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	79.7189	472	1314	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	79.2138	158	1314	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	78.8185	348	1314	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	78.5254	288	1314	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	78.427	227	1314	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	78.3593	235	1314	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.1887	278	1314	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.9889	335	1314	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.7958	170	1314	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.6921	263	1314	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	77.5281	216	1314	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.5128	192	1314	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4583	256	1314	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.7505	129	1314	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.7505	129	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,329] [INFO] DFAST Taxonomy check result was written to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:40:34,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:34,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:34,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/checkm_data
[2024-01-24 12:40:34,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:34,368] [INFO] Task started: CheckM
[2024-01-24 12:40:34,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/checkm_input GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/checkm_result
[2024-01-24 12:41:14,814] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:14,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:14,831] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:14,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:14,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:41:14,832] [INFO] Task started: Blastn
[2024-01-24 12:41:14,832] [INFO] Running command: blastn -query GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg87b04ec3-92d6-47dd-bebb-1bfac1719cbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:15,888] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:15,891] [INFO] Selected 11 target genomes.
[2024-01-24 12:41:15,892] [INFO] Target genome list was writen to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:15,899] [INFO] Task started: fastANI
[2024-01-24 12:41:15,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9806faf-a352-403d-a7d6-943062839abe/GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna.gz --refList GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:24,087] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:24,096] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:24,097] [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_001458175.1	s__Shimia marina	100.0	1309	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	conclusive
GCF_017743735.1	s__Shimia sp017743735	82.031	767	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_017744095.1	s__Shimia sp017744095	81.7829	718	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872815.1	s__Shimia sp014872815	80.4502	698	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	97.10	97.10	0.91	0.91	2	-
GCA_900537125.1	s__Shimia sp900537125	79.9582	632	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	79.6856	475	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346865.1	s__Shimia isoporae	78.8185	348	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458335.1	s__Cognatishimia activa	78.3418	235	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000169455.1	s__Pseudophaeobacter sp000169455	77.5798	256	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032505.1	s__Ruegeria atlantica_F	77.1185	204	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500075.1	s__Lentibacter sp018500075	76.507	168	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:24,099] [INFO] GTDB search result was written to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:24,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:24,103] [INFO] DFAST_QC result json was written to GCF_001458175.1_S.marinaCECT7688_Velvet_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:41:24,103] [INFO] DFAST_QC completed!
[2024-01-24 12:41:24,103] [INFO] Total running time: 0h1m17s