[2024-01-24 13:13:33,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:33,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:33,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference
[2024-01-24 13:13:34,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:34,323] [INFO] Task started: Prodigal
[2024-01-24 13:13:34,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg13a0eb24-99e2-4a6e-91e6-9c20ce905aa4/GCF_001641755.2_ASM164175v2_genomic.fna.gz | prodigal -d GCF_001641755.2_ASM164175v2_genomic.fna/cds.fna -a GCF_001641755.2_ASM164175v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:45,546] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:45,546] [INFO] Task started: HMMsearch
[2024-01-24 13:13:45,546] [INFO] Running command: hmmsearch --tblout GCF_001641755.2_ASM164175v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/reference_markers.hmm GCF_001641755.2_ASM164175v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:45,819] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:45,820] [INFO] Found 6/6 markers.
[2024-01-24 13:13:45,851] [INFO] Query marker FASTA was written to GCF_001641755.2_ASM164175v2_genomic.fna/markers.fasta
[2024-01-24 13:13:45,852] [INFO] Task started: Blastn
[2024-01-24 13:13:45,852] [INFO] Running command: blastn -query GCF_001641755.2_ASM164175v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/reference_markers.fasta -out GCF_001641755.2_ASM164175v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:46,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:46,684] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:46,685] [INFO] Target genome list was writen to GCF_001641755.2_ASM164175v2_genomic.fna/target_genomes.txt
[2024-01-24 13:13:46,716] [INFO] Task started: fastANI
[2024-01-24 13:13:46,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a0eb24-99e2-4a6e-91e6-9c20ce905aa4/GCF_001641755.2_ASM164175v2_genomic.fna.gz --refList GCF_001641755.2_ASM164175v2_genomic.fna/target_genomes.txt --output GCF_001641755.2_ASM164175v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:57,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:57,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:57,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:57,927] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:57,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:57,928] [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
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	100.0	1205	1207	95	conclusive
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	83.4623	907	1207	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	80.4079	630	1207	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	80.2372	608	1207	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	80.2319	614	1207	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	80.1921	602	1207	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	79.9184	581	1207	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	79.6615	565	1207	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	79.18	432	1207	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	79.1668	421	1207	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	79.0625	456	1207	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	78.9355	440	1207	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.0133	163	1207	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7196	155	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,929] [INFO] DFAST Taxonomy check result was written to GCF_001641755.2_ASM164175v2_genomic.fna/tc_result.tsv
[2024-01-24 13:13:57,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:57,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:57,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/checkm_data
[2024-01-24 13:13:57,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:57,989] [INFO] Task started: CheckM
[2024-01-24 13:13:57,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001641755.2_ASM164175v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001641755.2_ASM164175v2_genomic.fna/checkm_input GCF_001641755.2_ASM164175v2_genomic.fna/checkm_result
[2024-01-24 13:14:33,800] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:33,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,823] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:33,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:33,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001641755.2_ASM164175v2_genomic.fna/markers.fasta)
[2024-01-24 13:14:33,824] [INFO] Task started: Blastn
[2024-01-24 13:14:33,825] [INFO] Running command: blastn -query GCF_001641755.2_ASM164175v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d5b5881-3e35-47c1-b67f-01522d63dd56/dqc_reference/reference_markers_gtdb.fasta -out GCF_001641755.2_ASM164175v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:35,244] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:35,249] [INFO] Selected 9 target genomes.
[2024-01-24 13:14:35,250] [INFO] Target genome list was writen to GCF_001641755.2_ASM164175v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:35,281] [INFO] Task started: fastANI
[2024-01-24 13:14:35,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a0eb24-99e2-4a6e-91e6-9c20ce905aa4/GCF_001641755.2_ASM164175v2_genomic.fna.gz --refList GCF_001641755.2_ASM164175v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001641755.2_ASM164175v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:43,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:43,325] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:43,325] [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_001641755.2	s__Microbulbifer flavimaris	100.0	1205	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001750105.1	s__Microbulbifer aggregans	83.4612	908	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	80.3982	632	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100355.1	s__Microbulbifer yueqingensis	80.2282	608	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107725.1	s__Microbulbifer marinus	80.2164	615	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	80.1834	603	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	79.9261	579	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	79.6605	564	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002959965.1	s__Microbulbifer pacificus	79.1814	442	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:43,327] [INFO] GTDB search result was written to GCF_001641755.2_ASM164175v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:43,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:43,332] [INFO] DFAST_QC result json was written to GCF_001641755.2_ASM164175v2_genomic.fna/dqc_result.json
[2024-01-24 13:14:43,332] [INFO] DFAST_QC completed!
[2024-01-24 13:14:43,332] [INFO] Total running time: 0h1m10s