[2024-01-24 12:51:04,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:04,999] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:04,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference
[2024-01-24 12:51:06,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,191] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fc7f2a3-c688-433a-b025-f75ca16dddf9/GCF_017815515.1_ASM1781551v1_genomic.fna.gz | prodigal -d GCF_017815515.1_ASM1781551v1_genomic.fna/cds.fna -a GCF_017815515.1_ASM1781551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:17,181] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:17,182] [INFO] Task started: HMMsearch
[2024-01-24 12:51:17,182] [INFO] Running command: hmmsearch --tblout GCF_017815515.1_ASM1781551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/reference_markers.hmm GCF_017815515.1_ASM1781551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:17,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:17,437] [INFO] Found 6/6 markers.
[2024-01-24 12:51:17,472] [INFO] Query marker FASTA was written to GCF_017815515.1_ASM1781551v1_genomic.fna/markers.fasta
[2024-01-24 12:51:17,473] [INFO] Task started: Blastn
[2024-01-24 12:51:17,473] [INFO] Running command: blastn -query GCF_017815515.1_ASM1781551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/reference_markers.fasta -out GCF_017815515.1_ASM1781551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:18,444] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:18,448] [INFO] Selected 19 target genomes.
[2024-01-24 12:51:18,449] [INFO] Target genome list was writen to GCF_017815515.1_ASM1781551v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:18,462] [INFO] Task started: fastANI
[2024-01-24 12:51:18,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc7f2a3-c688-433a-b025-f75ca16dddf9/GCF_017815515.1_ASM1781551v1_genomic.fna.gz --refList GCF_017815515.1_ASM1781551v1_genomic.fna/target_genomes.txt --output GCF_017815515.1_ASM1781551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:34,512] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:34,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:34,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:34,532] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:34,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:34,533] [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 populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	100.0	1273	1274	95	conclusive
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	81.5157	661	1274	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	80.0588	593	1274	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	79.9541	611	1274	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	79.9527	590	1274	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	79.9032	596	1274	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	79.5207	558	1274	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.3904	525	1274	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	79.3086	501	1274	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	79.3018	516	1274	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	79.2597	523	1274	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.1087	520	1274	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_900141975.1	370622	370622	type	True	78.8477	497	1274	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	78.6433	517	1274	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.4222	403	1274	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.0787	392	1274	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.9615	377	1274	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	76.9371	298	1274	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	76.4642	302	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:34,534] [INFO] DFAST Taxonomy check result was written to GCF_017815515.1_ASM1781551v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:34,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:34,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:34,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/checkm_data
[2024-01-24 12:51:34,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:34,572] [INFO] Task started: CheckM
[2024-01-24 12:51:34,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017815515.1_ASM1781551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017815515.1_ASM1781551v1_genomic.fna/checkm_input GCF_017815515.1_ASM1781551v1_genomic.fna/checkm_result
[2024-01-24 12:52:14,051] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:14,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:14,070] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:14,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:14,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017815515.1_ASM1781551v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:14,071] [INFO] Task started: Blastn
[2024-01-24 12:52:14,071] [INFO] Running command: blastn -query GCF_017815515.1_ASM1781551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b917af7-8d9b-4571-a1d9-6f876acc7bab/dqc_reference/reference_markers_gtdb.fasta -out GCF_017815515.1_ASM1781551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:15,974] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:15,978] [INFO] Selected 16 target genomes.
[2024-01-24 12:52:15,978] [INFO] Target genome list was writen to GCF_017815515.1_ASM1781551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:16,023] [INFO] Task started: fastANI
[2024-01-24 12:52:16,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc7f2a3-c688-433a-b025-f75ca16dddf9/GCF_017815515.1_ASM1781551v1_genomic.fna.gz --refList GCF_017815515.1_ASM1781551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017815515.1_ASM1781551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:30,960] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:30,985] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:30,985] [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_017815515.1	s__Aureimonas populi	100.0	1274	1274	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_014058705.1	s__Aureimonas mangrovi	81.5185	659	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	80.0214	596	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583935.1	s__Aureimonas flava	79.9679	608	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	79.9095	593	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001463705.1	s__Aureimonas sp001463705	79.6341	574	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463745.1	s__Aureimonas sp001463745	79.6117	562	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442755.1	s__Aureimonas sp001442755	79.6054	605	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	98.47	96.94	0.96	0.92	3	-
GCF_001463765.1	s__Aureimonas sp001463765	79.5747	549	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	79.5676	538	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_010500835.1	s__Aurantimonas aggregata	79.4096	523	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425485.1	s__Aureimonas_A sp001425485	79.3914	593	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009765365.1	s__VTOM01 sp009765365	79.3216	573	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643375.1	s__Aureimonas_A glaciei	79.1798	562	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	78.6369	497	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167365.1	s__Consotaella salsifontis	78.3456	382	1274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Consotaella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:30,987] [INFO] GTDB search result was written to GCF_017815515.1_ASM1781551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:30,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:30,992] [INFO] DFAST_QC result json was written to GCF_017815515.1_ASM1781551v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:30,992] [INFO] DFAST_QC completed!
[2024-01-24 12:52:30,992] [INFO] Total running time: 0h1m26s