[2024-01-25 20:07:50,461] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:50,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:50,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference
[2024-01-25 20:07:51,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:51,617] [INFO] Task started: Prodigal
[2024-01-25 20:07:51,617] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9f9f791-6fe8-4e9e-ace2-65d9a4fedcce/GCF_001752425.1_ASM175242v1_genomic.fna.gz | prodigal -d GCF_001752425.1_ASM175242v1_genomic.fna/cds.fna -a GCF_001752425.1_ASM175242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:00,541] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:00,541] [INFO] Task started: HMMsearch
[2024-01-25 20:08:00,542] [INFO] Running command: hmmsearch --tblout GCF_001752425.1_ASM175242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/reference_markers.hmm GCF_001752425.1_ASM175242v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:00,769] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:00,770] [INFO] Found 6/6 markers.
[2024-01-25 20:08:00,795] [INFO] Query marker FASTA was written to GCF_001752425.1_ASM175242v1_genomic.fna/markers.fasta
[2024-01-25 20:08:00,796] [INFO] Task started: Blastn
[2024-01-25 20:08:00,796] [INFO] Running command: blastn -query GCF_001752425.1_ASM175242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/reference_markers.fasta -out GCF_001752425.1_ASM175242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:01,403] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:01,405] [INFO] Selected 10 target genomes.
[2024-01-25 20:08:01,405] [INFO] Target genome list was writen to GCF_001752425.1_ASM175242v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:01,409] [INFO] Task started: fastANI
[2024-01-25 20:08:01,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f9f791-6fe8-4e9e-ace2-65d9a4fedcce/GCF_001752425.1_ASM175242v1_genomic.fna.gz --refList GCF_001752425.1_ASM175242v1_genomic.fna/target_genomes.txt --output GCF_001752425.1_ASM175242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:08,674] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:08,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:08,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:08,682] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:08:08,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:08,682] [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
Salegentibacter salarius	strain=KCTC 12974	GCA_001752425.1	435906	435906	type	True	100.0	1080	1081	95	conclusive
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	99.9956	1074	1081	95	conclusive
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	99.9928	1076	1081	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	92.4611	960	1081	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	92.4288	958	1081	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	85.5108	856	1081	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	83.5681	823	1081	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.9116	50	1081	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.408	55	1081	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.2138	89	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:08,683] [INFO] DFAST Taxonomy check result was written to GCF_001752425.1_ASM175242v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:08,684] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:08,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:08,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/checkm_data
[2024-01-25 20:08:08,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:08,720] [INFO] Task started: CheckM
[2024-01-25 20:08:08,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001752425.1_ASM175242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001752425.1_ASM175242v1_genomic.fna/checkm_input GCF_001752425.1_ASM175242v1_genomic.fna/checkm_result
[2024-01-25 20:08:37,630] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:37,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:37,647] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:37,648] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:37,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001752425.1_ASM175242v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:37,649] [INFO] Task started: Blastn
[2024-01-25 20:08:37,649] [INFO] Running command: blastn -query GCF_001752425.1_ASM175242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f1b40e7-a63c-458c-b7ed-49d0b8587c15/dqc_reference/reference_markers_gtdb.fasta -out GCF_001752425.1_ASM175242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:38,498] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:38,500] [INFO] Selected 8 target genomes.
[2024-01-25 20:08:38,500] [INFO] Target genome list was writen to GCF_001752425.1_ASM175242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:38,510] [INFO] Task started: fastANI
[2024-01-25 20:08:38,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9f9f791-6fe8-4e9e-ace2-65d9a4fedcce/GCF_001752425.1_ASM175242v1_genomic.fna.gz --refList GCF_001752425.1_ASM175242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001752425.1_ASM175242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:45,467] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:45,472] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:45,473] [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_900168265.1	s__Salegentibacter salarius	99.9956	1074	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	conclusive
GCF_002900095.1	s__Salegentibacter mishustinae	92.4681	960	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900168045.1	s__Salegentibacter holothuriorum	87.5254	881	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	85.9224	839	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900142975.1	s__Salegentibacter salegens	85.3986	870	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.2523	834	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168115.1	s__Salegentibacter salinarum	83.4878	807	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016236915.1	s__Salegentibacter maritimus	83.2447	795	1081	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:45,474] [INFO] GTDB search result was written to GCF_001752425.1_ASM175242v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:45,474] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:45,477] [INFO] DFAST_QC result json was written to GCF_001752425.1_ASM175242v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:45,477] [INFO] DFAST_QC completed!
[2024-01-25 20:08:45,477] [INFO] Total running time: 0h0m55s