[2024-01-24 10:57:13,276] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,277] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference
[2024-01-24 10:57:14,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,792] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde44c04-b1af-4650-acbe-e03720ccb7a7/GCF_002087295.1_ASM208729v1_genomic.fna.gz | prodigal -d GCF_002087295.1_ASM208729v1_genomic.fna/cds.fna -a GCF_002087295.1_ASM208729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:24,968] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:24,968] [INFO] Task started: HMMsearch
[2024-01-24 10:57:24,968] [INFO] Running command: hmmsearch --tblout GCF_002087295.1_ASM208729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/reference_markers.hmm GCF_002087295.1_ASM208729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:25,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:25,225] [INFO] Found 6/6 markers.
[2024-01-24 10:57:25,268] [INFO] Query marker FASTA was written to GCF_002087295.1_ASM208729v1_genomic.fna/markers.fasta
[2024-01-24 10:57:25,269] [INFO] Task started: Blastn
[2024-01-24 10:57:25,269] [INFO] Running command: blastn -query GCF_002087295.1_ASM208729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/reference_markers.fasta -out GCF_002087295.1_ASM208729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:26,036] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:26,038] [INFO] Selected 5 target genomes.
[2024-01-24 10:57:26,039] [INFO] Target genome list was writen to GCF_002087295.1_ASM208729v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:26,042] [INFO] Task started: fastANI
[2024-01-24 10:57:26,042] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde44c04-b1af-4650-acbe-e03720ccb7a7/GCF_002087295.1_ASM208729v1_genomic.fna.gz --refList GCF_002087295.1_ASM208729v1_genomic.fna/target_genomes.txt --output GCF_002087295.1_ASM208729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:30,517] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:30,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:30,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:30,524] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:30,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:30,524] [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 lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	100.0	1158	1166	95	conclusive
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	94.7217	823	1166	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	94.6803	807	1166	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	94.5051	859	1166	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	87.8373	875	1166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:30,525] [INFO] DFAST Taxonomy check result was written to GCF_002087295.1_ASM208729v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:30,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:30,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:30,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/checkm_data
[2024-01-24 10:57:30,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:30,565] [INFO] Task started: CheckM
[2024-01-24 10:57:30,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002087295.1_ASM208729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002087295.1_ASM208729v1_genomic.fna/checkm_input GCF_002087295.1_ASM208729v1_genomic.fna/checkm_result
[2024-01-24 10:58:04,342] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:04,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:04,391] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:04,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:04,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002087295.1_ASM208729v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:04,392] [INFO] Task started: Blastn
[2024-01-24 10:58:04,392] [INFO] Running command: blastn -query GCF_002087295.1_ASM208729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5821e336-2095-46e1-a6ae-725b3d8ad89d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002087295.1_ASM208729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:05,483] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:05,487] [INFO] Selected 8 target genomes.
[2024-01-24 10:58:05,488] [INFO] Target genome list was writen to GCF_002087295.1_ASM208729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:05,493] [INFO] Task started: fastANI
[2024-01-24 10:58:05,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde44c04-b1af-4650-acbe-e03720ccb7a7/GCF_002087295.1_ASM208729v1_genomic.fna.gz --refList GCF_002087295.1_ASM208729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002087295.1_ASM208729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:12,220] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,232] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:12,233] [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_002087295.1	s__Halomonas lionensis	100.0	1158	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110265.1	s__Halomonas aquamarina	94.7217	823	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_009846525.1	s__Halomonas sp002696125	88.6268	868	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_014640815.1	s__Halomonas lutescens	87.8373	875	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012427705.1	s__Halomonas piezotolerans	85.5103	842	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014651775.1	s__Halomonas hamiltonii	82.2389	689	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_002966495.1	s__Halomonas sp002966495	81.282	559	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007989605.1	s__Halomonas venusta	80.474	514	1166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.80	96.64	0.92	0.83	8	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,235] [INFO] GTDB search result was written to GCF_002087295.1_ASM208729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:12,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:12,239] [INFO] DFAST_QC result json was written to GCF_002087295.1_ASM208729v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:12,239] [INFO] DFAST_QC completed!
[2024-01-24 10:58:12,239] [INFO] Total running time: 0h0m59s