[2024-01-25 20:12:05,815] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference
[2024-01-25 20:12:07,047] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,048] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d006a5f-f18e-4546-8720-ec528c321900/GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/cds.fna -a GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:16,868] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:16,868] [INFO] Task started: HMMsearch
[2024-01-25 20:12:16,869] [INFO] Running command: hmmsearch --tblout GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/reference_markers.hmm GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:17,101] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:17,101] [INFO] Found 6/6 markers.
[2024-01-25 20:12:17,132] [INFO] Query marker FASTA was written to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:12:17,133] [INFO] Task started: Blastn
[2024-01-25 20:12:17,133] [INFO] Running command: blastn -query GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/reference_markers.fasta -out GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:17,677] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:17,681] [INFO] Selected 14 target genomes.
[2024-01-25 20:12:17,681] [INFO] Target genome list was writen to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:12:17,687] [INFO] Task started: fastANI
[2024-01-25 20:12:17,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d006a5f-f18e-4546-8720-ec528c321900/GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna.gz --refList GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:26,513] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:26,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:26,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:26,521] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:26,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:26,521] [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
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	100.0	1286	1288	95	conclusive
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	80.2011	525	1288	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	80.0202	529	1288	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.8395	537	1288	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.839	526	1288	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.3323	453	1288	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	79.1022	438	1288	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	78.85	321	1288	95	below_threshold
Planococcus salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	78.7128	326	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:26,523] [INFO] DFAST Taxonomy check result was written to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:12:26,523] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:26,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:26,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/checkm_data
[2024-01-25 20:12:26,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:26,568] [INFO] Task started: CheckM
[2024-01-25 20:12:26,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/checkm_input GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:12:57,751] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:57,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:57,782] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:57,782] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:57,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:12:57,782] [INFO] Task started: Blastn
[2024-01-25 20:12:57,783] [INFO] Running command: blastn -query GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg754556fe-0b49-493b-befc-611db01f8c1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:58,586] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:58,589] [INFO] Selected 17 target genomes.
[2024-01-25 20:12:58,589] [INFO] Target genome list was writen to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:58,617] [INFO] Task started: fastANI
[2024-01-25 20:12:58,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d006a5f-f18e-4546-8720-ec528c321900/GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna.gz --refList GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:10,647] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:10,656] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:13:10,656] [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_900099655.1	s__Planococcus glaciei	100.0	1286	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.05	96.92	0.90	0.89	5	conclusive
GCF_016908095.1	s__Planococcus chinensis	80.496	584	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821325.1	s__Planococcus massiliensis	80.2118	524	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004761975.1	s__Planococcus koreensis	79.8187	525	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014836985.1	s__Planococcus sp014836985	79.3426	452	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	-
GCF_007859395.1	s__Planococcus sp007859395	79.2057	427	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873465.1	s__Planococcus mcmeekinii	79.1709	339	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859295.1	s__Planococcus sp007859295	79.1569	390	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859275.1	s__Planococcus sp007859275	79.125	449	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016881065.1	s__Planococcus soli	79.1084	438	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016820495.1	s__Planococcus sp016820495	78.9888	336	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613575.1	s__Planococcus sp018613575	78.9118	408	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001465795.2	s__Planococcus rifietoensis	78.8562	320	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719725.1	s__Planococcus salinus	78.5418	359	1288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:10,658] [INFO] GTDB search result was written to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:10,658] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:10,661] [INFO] DFAST_QC result json was written to GCF_900099655.1_IMG-taxon_2617270782_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:13:10,661] [INFO] DFAST_QC completed!
[2024-01-25 20:13:10,661] [INFO] Total running time: 0h1m5s