[2024-01-25 20:20:05,652] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference
[2024-01-25 20:20:06,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:06,782] [INFO] Task started: Prodigal
[2024-01-25 20:20:06,782] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2ba1a34-b89d-40eb-8268-daf084187b03/GCF_014196845.1_ASM1419684v1_genomic.fna.gz | prodigal -d GCF_014196845.1_ASM1419684v1_genomic.fna/cds.fna -a GCF_014196845.1_ASM1419684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:19,714] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:19,715] [INFO] Task started: HMMsearch
[2024-01-25 20:20:19,715] [INFO] Running command: hmmsearch --tblout GCF_014196845.1_ASM1419684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/reference_markers.hmm GCF_014196845.1_ASM1419684v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:20,007] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:20,008] [INFO] Found 6/6 markers.
[2024-01-25 20:20:20,051] [INFO] Query marker FASTA was written to GCF_014196845.1_ASM1419684v1_genomic.fna/markers.fasta
[2024-01-25 20:20:20,051] [INFO] Task started: Blastn
[2024-01-25 20:20:20,051] [INFO] Running command: blastn -query GCF_014196845.1_ASM1419684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/reference_markers.fasta -out GCF_014196845.1_ASM1419684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:21,127] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:21,130] [INFO] Selected 11 target genomes.
[2024-01-25 20:20:21,131] [INFO] Target genome list was writen to GCF_014196845.1_ASM1419684v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:21,146] [INFO] Task started: fastANI
[2024-01-25 20:20:21,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ba1a34-b89d-40eb-8268-daf084187b03/GCF_014196845.1_ASM1419684v1_genomic.fna.gz --refList GCF_014196845.1_ASM1419684v1_genomic.fna/target_genomes.txt --output GCF_014196845.1_ASM1419684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:33,584] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:33,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:33,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:33,593] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:33,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:33,593] [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
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	100.0	1675	1675	95	conclusive
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	99.9999	1675	1675	95	conclusive
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	90.3834	1241	1675	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	82.2789	877	1675	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	82.2381	870	1675	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	80.9581	776	1675	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	80.8797	809	1675	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	80.6768	810	1675	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	80.6719	733	1675	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.0927	452	1675	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.9608	368	1675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:33,596] [INFO] DFAST Taxonomy check result was written to GCF_014196845.1_ASM1419684v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:33,596] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:33,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:33,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/checkm_data
[2024-01-25 20:20:33,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:33,645] [INFO] Task started: CheckM
[2024-01-25 20:20:33,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196845.1_ASM1419684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196845.1_ASM1419684v1_genomic.fna/checkm_input GCF_014196845.1_ASM1419684v1_genomic.fna/checkm_result
[2024-01-25 20:21:13,445] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:13,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:13,468] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:13,468] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:13,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196845.1_ASM1419684v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:13,469] [INFO] Task started: Blastn
[2024-01-25 20:21:13,469] [INFO] Running command: blastn -query GCF_014196845.1_ASM1419684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2aad571d-5dcf-4251-a517-11be6e019af3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196845.1_ASM1419684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:15,649] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:15,652] [INFO] Selected 14 target genomes.
[2024-01-25 20:21:15,652] [INFO] Target genome list was writen to GCF_014196845.1_ASM1419684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:15,664] [INFO] Task started: fastANI
[2024-01-25 20:21:15,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ba1a34-b89d-40eb-8268-daf084187b03/GCF_014196845.1_ASM1419684v1_genomic.fna.gz --refList GCF_014196845.1_ASM1419684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196845.1_ASM1419684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:31,223] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:31,232] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:31,233] [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_014196845.1	s__Aurantimonas endophytica	100.0	1675	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010500835.1	s__Aurantimonas aggregata	90.3708	1242	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	82.3184	896	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_000153465.1	s__Aurantimonas manganoxydans	82.3023	875	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_002088275.1	s__Jiella sp002088275	81.1529	866	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	80.9728	806	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	80.9439	779	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	80.8933	809	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	80.7444	727	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_017183135.1	s__Aurantimonas sp017183135	80.6634	734	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	80.6607	812	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765365.1	s__VTOM01 sp009765365	79.7388	682	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	79.6227	633	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	79.4611	558	1675	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:31,234] [INFO] GTDB search result was written to GCF_014196845.1_ASM1419684v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:31,235] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:31,238] [INFO] DFAST_QC result json was written to GCF_014196845.1_ASM1419684v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:31,238] [INFO] DFAST_QC completed!
[2024-01-25 20:21:31,238] [INFO] Total running time: 0h1m26s