[2024-01-24 13:36:45,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,627] [INFO] DQC Reference Directory: /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference
[2024-01-24 13:36:46,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,917] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc3e404f-9daa-4042-b470-92bfe5ab6a17/GCF_000236035.1_KUC0.1_genomic.fna.gz | prodigal -d GCF_000236035.1_KUC0.1_genomic.fna/cds.fna -a GCF_000236035.1_KUC0.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:58,321] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:58,321] [INFO] Task started: HMMsearch
[2024-01-24 13:36:58,321] [INFO] Running command: hmmsearch --tblout GCF_000236035.1_KUC0.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/reference_markers.hmm GCF_000236035.1_KUC0.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:58,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:58,705] [INFO] Found 6/6 markers.
[2024-01-24 13:36:58,742] [INFO] Query marker FASTA was written to GCF_000236035.1_KUC0.1_genomic.fna/markers.fasta
[2024-01-24 13:36:58,743] [INFO] Task started: Blastn
[2024-01-24 13:36:58,743] [INFO] Running command: blastn -query GCF_000236035.1_KUC0.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/reference_markers.fasta -out GCF_000236035.1_KUC0.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:59,440] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:59,444] [INFO] Selected 11 target genomes.
[2024-01-24 13:36:59,445] [INFO] Target genome list was writen to GCF_000236035.1_KUC0.1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:59,450] [INFO] Task started: fastANI
[2024-01-24 13:36:59,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc3e404f-9daa-4042-b470-92bfe5ab6a17/GCF_000236035.1_KUC0.1_genomic.fna.gz --refList GCF_000236035.1_KUC0.1_genomic.fna/target_genomes.txt --output GCF_000236035.1_KUC0.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:09,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:09,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:09,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:09,528] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:09,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:09,529] [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
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	99.9804	1372	1394	95	conclusive
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	99.9527	1357	1394	95	conclusive
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	87.9228	1093	1394	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	87.6237	1092	1394	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	85.2324	1007	1394	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	84.0556	960	1394	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.2613	743	1394	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.2281	724	1394	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.4386	509	1394	95	below_threshold
Chromohalobacter moromii	strain=TMW 2.2308	GCA_023091865.1	2860329	2860329	type	True	77.0879	141	1394	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	77.0855	132	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:09,534] [INFO] DFAST Taxonomy check result was written to GCF_000236035.1_KUC0.1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:09,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:09,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:09,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/checkm_data
[2024-01-24 13:37:09,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:09,587] [INFO] Task started: CheckM
[2024-01-24 13:37:09,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000236035.1_KUC0.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000236035.1_KUC0.1_genomic.fna/checkm_input GCF_000236035.1_KUC0.1_genomic.fna/checkm_result
[2024-01-24 13:37:48,088] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:48,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:48,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:48,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:48,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000236035.1_KUC0.1_genomic.fna/markers.fasta)
[2024-01-24 13:37:48,111] [INFO] Task started: Blastn
[2024-01-24 13:37:48,111] [INFO] Running command: blastn -query GCF_000236035.1_KUC0.1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e5ed97-23ba-4588-99dc-8db8f5927f3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000236035.1_KUC0.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:49,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:49,262] [INFO] Selected 8 target genomes.
[2024-01-24 13:37:49,262] [INFO] Target genome list was writen to GCF_000236035.1_KUC0.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:49,275] [INFO] Task started: fastANI
[2024-01-24 13:37:49,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc3e404f-9daa-4042-b470-92bfe5ab6a17/GCF_000236035.1_KUC0.1_genomic.fna.gz --refList GCF_000236035.1_KUC0.1_genomic.fna/target_genomes_gtdb.txt --output GCF_000236035.1_KUC0.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:59,026] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:59,039] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:59,040] [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_000236035.1	s__Halomonas boliviensis	99.9804	1372	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCF_001882345.1	s__Halomonas sp001882345	89.6138	1069	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651035.1	s__Halomonas sp001651035	89.5572	1063	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.79	97.57	0.91	0.81	5	-
GCF_000336575.1	s__Halomonas titanicae	87.9054	1095	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_002257525.1	s__Halomonas ventosae_B	87.9034	1134	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_004364445.1	s__Halomonas alkaliantarctica	87.7897	1111	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_013416325.1	s__Halomonas sedimenti	87.6224	1092	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_002211105.1	s__Halomonas campaniensis_A	87.1056	1093	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,042] [INFO] GTDB search result was written to GCF_000236035.1_KUC0.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:59,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:59,045] [INFO] DFAST_QC result json was written to GCF_000236035.1_KUC0.1_genomic.fna/dqc_result.json
[2024-01-24 13:37:59,046] [INFO] DFAST_QC completed!
[2024-01-24 13:37:59,046] [INFO] Total running time: 0h1m13s