[2023-06-28 16:48:48,016] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:48:48,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:48:48,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference
[2023-06-28 16:48:49,328] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:48:49,329] [INFO] Task started: Prodigal
[2023-06-28 16:48:49,329] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3a694e4-73b8-4701-9dbf-8f6641fb4d61/GCA_020055635.1_ASM2005563v1_genomic.fna.gz | prodigal -d GCA_020055635.1_ASM2005563v1_genomic.fna/cds.fna -a GCA_020055635.1_ASM2005563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:49:04,158] [INFO] Task succeeded: Prodigal
[2023-06-28 16:49:04,158] [INFO] Task started: HMMsearch
[2023-06-28 16:49:04,159] [INFO] Running command: hmmsearch --tblout GCA_020055635.1_ASM2005563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/reference_markers.hmm GCA_020055635.1_ASM2005563v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:49:04,438] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:49:04,440] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc3a694e4-73b8-4701-9dbf-8f6641fb4d61/GCA_020055635.1_ASM2005563v1_genomic.fna.gz]
[2023-06-28 16:49:04,488] [INFO] Query marker FASTA was written to GCA_020055635.1_ASM2005563v1_genomic.fna/markers.fasta
[2023-06-28 16:49:04,489] [INFO] Task started: Blastn
[2023-06-28 16:49:04,489] [INFO] Running command: blastn -query GCA_020055635.1_ASM2005563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/reference_markers.fasta -out GCA_020055635.1_ASM2005563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:49:05,411] [INFO] Task succeeded: Blastn
[2023-06-28 16:49:05,414] [INFO] Selected 13 target genomes.
[2023-06-28 16:49:05,415] [INFO] Target genome list was writen to GCA_020055635.1_ASM2005563v1_genomic.fna/target_genomes.txt
[2023-06-28 16:49:05,418] [INFO] Task started: fastANI
[2023-06-28 16:49:05,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a694e4-73b8-4701-9dbf-8f6641fb4d61/GCA_020055635.1_ASM2005563v1_genomic.fna.gz --refList GCA_020055635.1_ASM2005563v1_genomic.fna/target_genomes.txt --output GCA_020055635.1_ASM2005563v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:49:16,304] [INFO] Task succeeded: fastANI
[2023-06-28 16:49:16,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:49:16,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:49:16,321] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:49:16,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:49:16,322] [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
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	84.4012	939	1547	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	82.1642	783	1547	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	82.1062	798	1547	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	81.8513	827	1547	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	79.9798	692	1547	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.7418	554	1547	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.7215	500	1547	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4265	388	1547	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2605	420	1547	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.1521	398	1547	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.0419	414	1547	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9194	405	1547	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.5923	366	1547	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:49:16,324] [INFO] DFAST Taxonomy check result was written to GCA_020055635.1_ASM2005563v1_genomic.fna/tc_result.tsv
[2023-06-28 16:49:16,324] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:49:16,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:49:16,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/checkm_data
[2023-06-28 16:49:16,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:49:16,371] [INFO] Task started: CheckM
[2023-06-28 16:49:16,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020055635.1_ASM2005563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020055635.1_ASM2005563v1_genomic.fna/checkm_input GCA_020055635.1_ASM2005563v1_genomic.fna/checkm_result
[2023-06-28 16:50:05,754] [INFO] Task succeeded: CheckM
[2023-06-28 16:50:05,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:50:05,778] [INFO] ===== Completeness check finished =====
[2023-06-28 16:50:05,779] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:50:05,779] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020055635.1_ASM2005563v1_genomic.fna/markers.fasta)
[2023-06-28 16:50:05,780] [INFO] Task started: Blastn
[2023-06-28 16:50:05,780] [INFO] Running command: blastn -query GCA_020055635.1_ASM2005563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d17c6d-5a6c-42b8-b9fd-df9a08c17ea4/dqc_reference/reference_markers_gtdb.fasta -out GCA_020055635.1_ASM2005563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:50:07,328] [INFO] Task succeeded: Blastn
[2023-06-28 16:50:07,333] [INFO] Selected 10 target genomes.
[2023-06-28 16:50:07,333] [INFO] Target genome list was writen to GCA_020055635.1_ASM2005563v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:50:07,342] [INFO] Task started: fastANI
[2023-06-28 16:50:07,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3a694e4-73b8-4701-9dbf-8f6641fb4d61/GCA_020055635.1_ASM2005563v1_genomic.fna.gz --refList GCA_020055635.1_ASM2005563v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020055635.1_ASM2005563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:50:16,345] [INFO] Task succeeded: fastANI
[2023-06-28 16:50:16,360] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:50:16,360] [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_014637725.1	s__Marivita lacus	84.4012	939	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	82.4399	762	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	82.1254	796	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002115725.1	s__Marivita cryptomonadis	81.8513	827	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	99.81	99.78	0.91	0.91	31	-
GCA_003149565.1	s__Marivita sp003149565	81.3857	708	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	79.9797	692	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	79.48	578	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.0764	549	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.7048	502	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.0507	413	1547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:50:16,362] [INFO] GTDB search result was written to GCA_020055635.1_ASM2005563v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:50:16,363] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:50:16,366] [INFO] DFAST_QC result json was written to GCA_020055635.1_ASM2005563v1_genomic.fna/dqc_result.json
[2023-06-28 16:50:16,367] [INFO] DFAST_QC completed!
[2023-06-28 16:50:16,367] [INFO] Total running time: 0h1m28s