[2024-01-25 20:15:20,747] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:20,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:20,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference
[2024-01-25 20:15:21,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:21,876] [INFO] Task started: Prodigal
[2024-01-25 20:15:21,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bbec6bf-8403-4d8a-ae2d-74116f812302/GCF_023698535.1_ASM2369853v1_genomic.fna.gz | prodigal -d GCF_023698535.1_ASM2369853v1_genomic.fna/cds.fna -a GCF_023698535.1_ASM2369853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:38,929] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:38,929] [INFO] Task started: HMMsearch
[2024-01-25 20:15:38,929] [INFO] Running command: hmmsearch --tblout GCF_023698535.1_ASM2369853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/reference_markers.hmm GCF_023698535.1_ASM2369853v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:39,142] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:39,143] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0bbec6bf-8403-4d8a-ae2d-74116f812302/GCF_023698535.1_ASM2369853v1_genomic.fna.gz]
[2024-01-25 20:15:39,176] [INFO] Query marker FASTA was written to GCF_023698535.1_ASM2369853v1_genomic.fna/markers.fasta
[2024-01-25 20:15:39,176] [INFO] Task started: Blastn
[2024-01-25 20:15:39,176] [INFO] Running command: blastn -query GCF_023698535.1_ASM2369853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/reference_markers.fasta -out GCF_023698535.1_ASM2369853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:39,675] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:39,678] [INFO] Selected 7 target genomes.
[2024-01-25 20:15:39,678] [INFO] Target genome list was writen to GCF_023698535.1_ASM2369853v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:39,681] [INFO] Task started: fastANI
[2024-01-25 20:15:39,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bbec6bf-8403-4d8a-ae2d-74116f812302/GCF_023698535.1_ASM2369853v1_genomic.fna.gz --refList GCF_023698535.1_ASM2369853v1_genomic.fna/target_genomes.txt --output GCF_023698535.1_ASM2369853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:46,589] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:46,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:46,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:46,595] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:46,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:46,596] [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
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	100.0	1316	1322	95	conclusive
Halorientalis persicus	strain=IBRC-M 10043	GCA_900110215.1	1367881	1367881	type	True	89.997	1009	1322	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	89.6043	979	1322	95	below_threshold
Halorientalis marina	strain=GDY88	GCA_023028345.1	2931976	2931976	type	True	81.0064	745	1322	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	80.7926	672	1322	95	below_threshold
Halorientalis salina	strain=NEN8	GCA_023566035.1	2932266	2932266	type	True	80.7594	676	1322	95	below_threshold
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	80.247	579	1322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:46,597] [INFO] DFAST Taxonomy check result was written to GCF_023698535.1_ASM2369853v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:46,598] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:46,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:46,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/checkm_data
[2024-01-25 20:15:46,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:46,638] [INFO] Task started: CheckM
[2024-01-25 20:15:46,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023698535.1_ASM2369853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023698535.1_ASM2369853v1_genomic.fna/checkm_input GCF_023698535.1_ASM2369853v1_genomic.fna/checkm_result
[2024-01-25 20:16:33,078] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:33,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:33,107] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:33,107] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:33,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023698535.1_ASM2369853v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:33,108] [INFO] Task started: Blastn
[2024-01-25 20:16:33,108] [INFO] Running command: blastn -query GCF_023698535.1_ASM2369853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfa6595f-855a-43a7-9c2f-345d7516ee10/dqc_reference/reference_markers_gtdb.fasta -out GCF_023698535.1_ASM2369853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:33,629] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:33,632] [INFO] Selected 6 target genomes.
[2024-01-25 20:16:33,632] [INFO] Target genome list was writen to GCF_023698535.1_ASM2369853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:33,636] [INFO] Task started: fastANI
[2024-01-25 20:16:33,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bbec6bf-8403-4d8a-ae2d-74116f812302/GCF_023698535.1_ASM2369853v1_genomic.fna.gz --refList GCF_023698535.1_ASM2369853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023698535.1_ASM2369853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:39,821] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:39,826] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:39,826] [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_900102305.1	s__Halorientalis regularis	99.9838	1299	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110215.1	s__Halorientalis persicus	89.9741	1010	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	89.605	979	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001989615.1	s__Halorientalis sp001989615	87.1844	879	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005049285.1	s__Halorientalis sp005049285	80.7608	675	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	78.4356	388	1322	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:39,829] [INFO] GTDB search result was written to GCF_023698535.1_ASM2369853v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:39,830] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:39,833] [INFO] DFAST_QC result json was written to GCF_023698535.1_ASM2369853v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:39,833] [INFO] DFAST_QC completed!
[2024-01-25 20:16:39,833] [INFO] Total running time: 0h1m19s