[2024-01-24 13:41:40,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference
[2024-01-24 13:41:42,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,060] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,060] [INFO] Running command: gunzip -c /var/lib/cwl/stgda0aacd5-fdd2-413d-97dd-b6b9d4edee9a/GCF_004357985.1_ASM435798v1_genomic.fna.gz | prodigal -d GCF_004357985.1_ASM435798v1_genomic.fna/cds.fna -a GCF_004357985.1_ASM435798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:55,083] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:55,083] [INFO] Task started: HMMsearch
[2024-01-24 13:41:55,084] [INFO] Running command: hmmsearch --tblout GCF_004357985.1_ASM435798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/reference_markers.hmm GCF_004357985.1_ASM435798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:55,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:55,366] [INFO] Found 6/6 markers.
[2024-01-24 13:41:55,404] [INFO] Query marker FASTA was written to GCF_004357985.1_ASM435798v1_genomic.fna/markers.fasta
[2024-01-24 13:41:55,404] [INFO] Task started: Blastn
[2024-01-24 13:41:55,405] [INFO] Running command: blastn -query GCF_004357985.1_ASM435798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/reference_markers.fasta -out GCF_004357985.1_ASM435798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:56,521] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:56,525] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:56,526] [INFO] Target genome list was writen to GCF_004357985.1_ASM435798v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:56,531] [INFO] Task started: fastANI
[2024-01-24 13:41:56,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0aacd5-fdd2-413d-97dd-b6b9d4edee9a/GCF_004357985.1_ASM435798v1_genomic.fna.gz --refList GCF_004357985.1_ASM435798v1_genomic.fna/target_genomes.txt --output GCF_004357985.1_ASM435798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:08,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:08,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:08,083] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:08,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:08,083] [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
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	100.0	1222	1225	95	conclusive
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	83.7334	797	1225	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	82.842	782	1225	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	82.8084	804	1225	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	82.1703	711	1225	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.8568	625	1225	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.785	632	1225	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.7342	623	1225	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.6099	610	1225	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.3237	676	1225	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	81.1252	656	1225	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	80.9464	604	1225	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.8672	576	1225	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	80.4156	586	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,085] [INFO] DFAST Taxonomy check result was written to GCF_004357985.1_ASM435798v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:08,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:08,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:08,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/checkm_data
[2024-01-24 13:42:08,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:08,127] [INFO] Task started: CheckM
[2024-01-24 13:42:08,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004357985.1_ASM435798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004357985.1_ASM435798v1_genomic.fna/checkm_input GCF_004357985.1_ASM435798v1_genomic.fna/checkm_result
[2024-01-24 13:42:54,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:54,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:55,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:55,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:55,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004357985.1_ASM435798v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:55,010] [INFO] Task started: Blastn
[2024-01-24 13:42:55,011] [INFO] Running command: blastn -query GCF_004357985.1_ASM435798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg507908dc-1e92-4729-aaf7-8aa63504ec66/dqc_reference/reference_markers_gtdb.fasta -out GCF_004357985.1_ASM435798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:57,094] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:57,098] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:57,098] [INFO] Target genome list was writen to GCF_004357985.1_ASM435798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:57,130] [INFO] Task started: fastANI
[2024-01-24 13:42:57,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0aacd5-fdd2-413d-97dd-b6b9d4edee9a/GCF_004357985.1_ASM435798v1_genomic.fna.gz --refList GCF_004357985.1_ASM435798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004357985.1_ASM435798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:08,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:08,221] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:08,222] [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_004357985.1	s__Luteimonas aestuarii	100.0	1222	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859325.1	s__Luteimonas marina	83.691	801	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016774335.1	s__Luteimonas sp016774335	82.8506	800	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	82.8312	783	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	82.4386	707	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	82.1785	710	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_000422305.1	s__Luteimonas mephitis	81.8338	626	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	81.7896	631	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	81.3133	677	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615955.1	s__Luteimonas sp016615955	81.2382	591	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	80.9321	607	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_004284195.1	s__Pseudoxanthomonas_A sp004284195	80.7647	592	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	97.94	97.04	0.92	0.87	11	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	80.5779	564	1225	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:08,223] [INFO] GTDB search result was written to GCF_004357985.1_ASM435798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:08,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:08,227] [INFO] DFAST_QC result json was written to GCF_004357985.1_ASM435798v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:08,227] [INFO] DFAST_QC completed!
[2024-01-24 13:43:08,227] [INFO] Total running time: 0h1m28s