[2024-01-25 19:46:06,059] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:06,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:06,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference
[2024-01-25 19:46:07,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:07,148] [INFO] Task started: Prodigal
[2024-01-25 19:46:07,149] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2f85d87-a8ce-4031-8e6c-524673297599/GCF_024171465.1_ASM2417146v1_genomic.fna.gz | prodigal -d GCF_024171465.1_ASM2417146v1_genomic.fna/cds.fna -a GCF_024171465.1_ASM2417146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:28,631] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:28,631] [INFO] Task started: HMMsearch
[2024-01-25 19:46:28,632] [INFO] Running command: hmmsearch --tblout GCF_024171465.1_ASM2417146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/reference_markers.hmm GCF_024171465.1_ASM2417146v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:28,929] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:28,930] [INFO] Found 6/6 markers.
[2024-01-25 19:46:28,986] [INFO] Query marker FASTA was written to GCF_024171465.1_ASM2417146v1_genomic.fna/markers.fasta
[2024-01-25 19:46:28,987] [INFO] Task started: Blastn
[2024-01-25 19:46:28,987] [INFO] Running command: blastn -query GCF_024171465.1_ASM2417146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/reference_markers.fasta -out GCF_024171465.1_ASM2417146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:30,003] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:30,005] [INFO] Selected 12 target genomes.
[2024-01-25 19:46:30,006] [INFO] Target genome list was writen to GCF_024171465.1_ASM2417146v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:30,014] [INFO] Task started: fastANI
[2024-01-25 19:46:30,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f85d87-a8ce-4031-8e6c-524673297599/GCF_024171465.1_ASM2417146v1_genomic.fna.gz --refList GCF_024171465.1_ASM2417146v1_genomic.fna/target_genomes.txt --output GCF_024171465.1_ASM2417146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:51,642] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:51,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:51,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:51,650] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:51,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:51,651] [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
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	90.9134	1850	2447	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	90.708	1833	2447	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	87.0309	1583	2447	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	86.0992	1486	2447	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	86.0156	1499	2447	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	85.1529	1521	2447	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	84.8707	1489	2447	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	84.1002	1292	2447	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	83.8627	1279	2447	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	83.7065	1257	2447	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	83.2272	1319	2447	95	below_threshold
Janthinobacterium tructae	strain=SNU WT3	GCA_006517255.1	2590869	2590869	type	True	80.745	1085	2447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:51,652] [INFO] DFAST Taxonomy check result was written to GCF_024171465.1_ASM2417146v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:51,652] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:51,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:51,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/checkm_data
[2024-01-25 19:46:51,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:51,724] [INFO] Task started: CheckM
[2024-01-25 19:46:51,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171465.1_ASM2417146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171465.1_ASM2417146v1_genomic.fna/checkm_input GCF_024171465.1_ASM2417146v1_genomic.fna/checkm_result
[2024-01-25 19:47:56,953] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:56,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:56,978] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:56,978] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:56,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171465.1_ASM2417146v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:56,980] [INFO] Task started: Blastn
[2024-01-25 19:47:56,980] [INFO] Running command: blastn -query GCF_024171465.1_ASM2417146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb92e9925-7a1c-4906-b6bd-3caef20dd3ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171465.1_ASM2417146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:59,055] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:59,058] [INFO] Selected 7 target genomes.
[2024-01-25 19:47:59,058] [INFO] Target genome list was writen to GCF_024171465.1_ASM2417146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:59,078] [INFO] Task started: fastANI
[2024-01-25 19:47:59,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2f85d87-a8ce-4031-8e6c-524673297599/GCF_024171465.1_ASM2417146v1_genomic.fna.gz --refList GCF_024171465.1_ASM2417146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171465.1_ASM2417146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:14,726] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:14,732] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:48:14,732] [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
GCA_000381565.1	s__Duganella sp000381565	94.9009	1935	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_003416895.1	s__Duganella sp003416895	93.7746	1946	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	99.92	99.92	0.99	0.99	2	-
GCF_003416985.1	s__Duganella sp003416985	91.2832	1855	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_000335815.1	s__Duganella sp000335815	90.7291	1858	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	-
GCF_009380215.1	s__Duganella sp009380215	90.6979	1834	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375995.1	s__Duganella sp013375995	88.9337	1764	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011090165.1	s__Duganella aceris	86.9877	1589	2447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:14,733] [INFO] GTDB search result was written to GCF_024171465.1_ASM2417146v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:14,734] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:14,736] [INFO] DFAST_QC result json was written to GCF_024171465.1_ASM2417146v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:14,737] [INFO] DFAST_QC completed!
[2024-01-25 19:48:14,737] [INFO] Total running time: 0h2m9s