[2024-01-25 20:05:05,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:05,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:05,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference
[2024-01-25 20:05:06,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:06,843] [INFO] Task started: Prodigal
[2024-01-25 20:05:06,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg60de4f00-e17e-49fc-a345-475e808a7847/GCF_014191725.1_ASM1419172v1_genomic.fna.gz | prodigal -d GCF_014191725.1_ASM1419172v1_genomic.fna/cds.fna -a GCF_014191725.1_ASM1419172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:22,374] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:22,375] [INFO] Task started: HMMsearch
[2024-01-25 20:05:22,375] [INFO] Running command: hmmsearch --tblout GCF_014191725.1_ASM1419172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/reference_markers.hmm GCF_014191725.1_ASM1419172v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:22,657] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:22,658] [INFO] Found 6/6 markers.
[2024-01-25 20:05:22,700] [INFO] Query marker FASTA was written to GCF_014191725.1_ASM1419172v1_genomic.fna/markers.fasta
[2024-01-25 20:05:22,700] [INFO] Task started: Blastn
[2024-01-25 20:05:22,700] [INFO] Running command: blastn -query GCF_014191725.1_ASM1419172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/reference_markers.fasta -out GCF_014191725.1_ASM1419172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:23,512] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:23,516] [INFO] Selected 13 target genomes.
[2024-01-25 20:05:23,516] [INFO] Target genome list was writen to GCF_014191725.1_ASM1419172v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:23,517] [INFO] Task started: fastANI
[2024-01-25 20:05:23,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg60de4f00-e17e-49fc-a345-475e808a7847/GCF_014191725.1_ASM1419172v1_genomic.fna.gz --refList GCF_014191725.1_ASM1419172v1_genomic.fna/target_genomes.txt --output GCF_014191725.1_ASM1419172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:36,327] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:36,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:36,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:36,337] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:36,337] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:36,337] [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 rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	100.0	1743	1744	95	conclusive
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	81.9615	848	1744	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	81.0989	732	1744	95	below_threshold
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	81.0182	714	1744	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	80.3877	715	1744	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	80.1543	625	1744	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	79.5868	573	1744	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	79.3137	616	1744	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	79.1661	489	1744	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	79.1289	488	1744	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	79.0062	521	1744	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.178	202	1744	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.9042	226	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:36,338] [INFO] DFAST Taxonomy check result was written to GCF_014191725.1_ASM1419172v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:36,339] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:36,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:36,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/checkm_data
[2024-01-25 20:05:36,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:36,405] [INFO] Task started: CheckM
[2024-01-25 20:05:36,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191725.1_ASM1419172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191725.1_ASM1419172v1_genomic.fna/checkm_input GCF_014191725.1_ASM1419172v1_genomic.fna/checkm_result
[2024-01-25 20:06:21,288] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:21,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:21,319] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:21,320] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:21,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191725.1_ASM1419172v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:21,321] [INFO] Task started: Blastn
[2024-01-25 20:06:21,321] [INFO] Running command: blastn -query GCF_014191725.1_ASM1419172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52679319-2821-4dac-9887-7e176030cf7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191725.1_ASM1419172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:22,818] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:22,821] [INFO] Selected 10 target genomes.
[2024-01-25 20:06:22,821] [INFO] Target genome list was writen to GCF_014191725.1_ASM1419172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:22,825] [INFO] Task started: fastANI
[2024-01-25 20:06:22,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg60de4f00-e17e-49fc-a345-475e808a7847/GCF_014191725.1_ASM1419172v1_genomic.fna.gz --refList GCF_014191725.1_ASM1419172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191725.1_ASM1419172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:32,787] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:32,794] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:32,795] [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_014191725.1	s__Microbulbifer rhizosphaerae	100.0	1742	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014904815.1	s__Microbulbifer taiwanensis	81.9739	847	1744	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	81.0766	735	1744	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	81.0089	715	1744	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	80.3712	717	1744	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	80.1447	627	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641755.2	s__Microbulbifer flavimaris	79.6062	570	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005771435.1	s__Microbulbifer harenosus	79.3294	614	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
GCF_009903625.1	s__Microbulbifer sp009903625	79.099	525	1744	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	79.0713	540	1744	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:32,796] [INFO] GTDB search result was written to GCF_014191725.1_ASM1419172v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:32,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:32,799] [INFO] DFAST_QC result json was written to GCF_014191725.1_ASM1419172v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:32,799] [INFO] DFAST_QC completed!
[2024-01-25 20:06:32,799] [INFO] Total running time: 0h1m27s