[2024-01-24 13:16:56,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference
[2024-01-24 13:16:57,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,532] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,533] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a18b9cf-027e-4335-90c4-40c4a89c7ea7/GCF_008369445.1_ASM836944v1_genomic.fna.gz | prodigal -d GCF_008369445.1_ASM836944v1_genomic.fna/cds.fna -a GCF_008369445.1_ASM836944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:10,778] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:10,778] [INFO] Task started: HMMsearch
[2024-01-24 13:17:10,778] [INFO] Running command: hmmsearch --tblout GCF_008369445.1_ASM836944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/reference_markers.hmm GCF_008369445.1_ASM836944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:11,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:11,055] [INFO] Found 6/6 markers.
[2024-01-24 13:17:11,094] [INFO] Query marker FASTA was written to GCF_008369445.1_ASM836944v1_genomic.fna/markers.fasta
[2024-01-24 13:17:11,094] [INFO] Task started: Blastn
[2024-01-24 13:17:11,094] [INFO] Running command: blastn -query GCF_008369445.1_ASM836944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/reference_markers.fasta -out GCF_008369445.1_ASM836944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:11,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:11,886] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:11,887] [INFO] Target genome list was writen to GCF_008369445.1_ASM836944v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:11,898] [INFO] Task started: fastANI
[2024-01-24 13:17:11,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a18b9cf-027e-4335-90c4-40c4a89c7ea7/GCF_008369445.1_ASM836944v1_genomic.fna.gz --refList GCF_008369445.1_ASM836944v1_genomic.fna/target_genomes.txt --output GCF_008369445.1_ASM836944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:28,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:28,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:28,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:28,108] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:28,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:28,108] [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
Aureimonas fodinaquatilis	strain=CAU 1482	GCA_008369445.1	2565783	2565783	type	True	100.0	1308	1309	95	conclusive
Aureimonas frigidaquae	strain=JCM 14755	GCA_001463905.1	424757	424757	type	True	77.1993	218	1309	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_900141975.1	370622	370622	type	True	77.1273	271	1309	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_001463885.1	370622	370622	type	True	77.0631	275	1309	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	76.7264	108	1309	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	76.7004	114	1309	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.6634	74	1309	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	76.6291	149	1309	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	76.5893	122	1309	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	76.5823	120	1309	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	76.4205	117	1309	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.1324	99	1309	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	76.0665	99	1309	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	76.0364	99	1309	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	76.0209	88	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:28,112] [INFO] DFAST Taxonomy check result was written to GCF_008369445.1_ASM836944v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:28,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:28,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:28,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/checkm_data
[2024-01-24 13:17:28,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:28,160] [INFO] Task started: CheckM
[2024-01-24 13:17:28,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008369445.1_ASM836944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008369445.1_ASM836944v1_genomic.fna/checkm_input GCF_008369445.1_ASM836944v1_genomic.fna/checkm_result
[2024-01-24 13:18:11,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:11,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:11,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:11,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:11,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008369445.1_ASM836944v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:11,033] [INFO] Task started: Blastn
[2024-01-24 13:18:11,033] [INFO] Running command: blastn -query GCF_008369445.1_ASM836944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc14e4b21-297c-41ea-8ab0-9f0867e544f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_008369445.1_ASM836944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:12,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:12,452] [INFO] Selected 22 target genomes.
[2024-01-24 13:18:12,452] [INFO] Target genome list was writen to GCF_008369445.1_ASM836944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:12,469] [INFO] Task started: fastANI
[2024-01-24 13:18:12,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a18b9cf-027e-4335-90c4-40c4a89c7ea7/GCF_008369445.1_ASM836944v1_genomic.fna.gz --refList GCF_008369445.1_ASM836944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008369445.1_ASM836944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:27,833] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:27,850] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:27,851] [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_008369445.1	s__Aureimonas fodinaquatilis	100.0	1308	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014844055.1	s__Aureimonas altamirensis_A	77.4094	254	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	97.71	97.71	0.89	0.89	2	-
GCF_001463905.1	s__Aureimonas frigidaquae	77.1993	218	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463885.1	s__Aureimonas altamirensis	77.0716	274	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000153465.1	s__Aurantimonas manganoxydans	77.0176	117	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_002893625.1	s__Mangrovicella endophytica	76.7107	109	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017183135.1	s__Aurantimonas sp017183135	76.7004	114	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815515.1	s__Aureimonas populi	76.6291	149	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	76.5893	122	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_000382705.1	s__Aureimonas ureilytica	76.5374	132	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002075885.1	s__Mesorhizobium manganicum	76.496	83	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	76.4372	98	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_014196845.1	s__Aurantimonas endophytica	76.4205	117	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829835.1	s__Neorhizobium sp002431175	76.3708	82	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.71	95.71	0.88	0.88	2	-
GCF_014643375.1	s__Aureimonas_A glaciei	76.2476	125	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	76.2122	101	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442685.1	s__Mesorhizobium sp006442685	76.1164	89	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.73	95.49	0.95	0.85	44	-
GCA_002316345.1	s__Corticibacterium sp002316345	76.0215	74	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,852] [INFO] GTDB search result was written to GCF_008369445.1_ASM836944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:27,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:27,859] [INFO] DFAST_QC result json was written to GCF_008369445.1_ASM836944v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:27,859] [INFO] DFAST_QC completed!
[2024-01-24 13:18:27,860] [INFO] Total running time: 0h1m32s