[2024-01-25 18:43:50,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:50,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:50,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference
[2024-01-25 18:43:51,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:51,619] [INFO] Task started: Prodigal
[2024-01-25 18:43:51,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg47de5002-f4a6-424a-8e20-ef66e54143e8/GCF_014643375.1_ASM1464337v1_genomic.fna.gz | prodigal -d GCF_014643375.1_ASM1464337v1_genomic.fna/cds.fna -a GCF_014643375.1_ASM1464337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:05,325] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:05,325] [INFO] Task started: HMMsearch
[2024-01-25 18:44:05,325] [INFO] Running command: hmmsearch --tblout GCF_014643375.1_ASM1464337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/reference_markers.hmm GCF_014643375.1_ASM1464337v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:05,662] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:05,663] [INFO] Found 6/6 markers.
[2024-01-25 18:44:05,706] [INFO] Query marker FASTA was written to GCF_014643375.1_ASM1464337v1_genomic.fna/markers.fasta
[2024-01-25 18:44:05,706] [INFO] Task started: Blastn
[2024-01-25 18:44:05,706] [INFO] Running command: blastn -query GCF_014643375.1_ASM1464337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/reference_markers.fasta -out GCF_014643375.1_ASM1464337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:06,650] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:06,653] [INFO] Selected 23 target genomes.
[2024-01-25 18:44:06,654] [INFO] Target genome list was writen to GCF_014643375.1_ASM1464337v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:06,666] [INFO] Task started: fastANI
[2024-01-25 18:44:06,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg47de5002-f4a6-424a-8e20-ef66e54143e8/GCF_014643375.1_ASM1464337v1_genomic.fna.gz --refList GCF_014643375.1_ASM1464337v1_genomic.fna/target_genomes.txt --output GCF_014643375.1_ASM1464337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:29,271] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:29,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:29,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:29,285] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:44:29,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:44:29,285] [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=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.7166	806	1864	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.7107	811	1864	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	80.5278	772	1864	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	80.5079	763	1864	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.4757	838	1864	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.3557	744	1864	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.3208	728	1864	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	80.2867	744	1864	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	80.2749	796	1864	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	80.0609	785	1864	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	79.9851	704	1864	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.8923	752	1864	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	79.5681	658	1864	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	79.5663	649	1864	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.3199	581	1864	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	79.2909	630	1864	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	79.2887	551	1864	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	79.1291	556	1864	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.9301	600	1864	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.2516	508	1864	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_001463885.1	370622	370622	type	True	78.2367	490	1864	95	below_threshold
Aureimonas altamirensis	strain=DSM 21988	GCA_900141975.1	370622	370622	type	True	78.2228	498	1864	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	76.5323	235	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:29,286] [INFO] DFAST Taxonomy check result was written to GCF_014643375.1_ASM1464337v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:29,287] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:29,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:29,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/checkm_data
[2024-01-25 18:44:29,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:29,342] [INFO] Task started: CheckM
[2024-01-25 18:44:29,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643375.1_ASM1464337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643375.1_ASM1464337v1_genomic.fna/checkm_input GCF_014643375.1_ASM1464337v1_genomic.fna/checkm_result
[2024-01-25 18:45:10,520] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:10,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:10,539] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:10,540] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:10,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643375.1_ASM1464337v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:10,540] [INFO] Task started: Blastn
[2024-01-25 18:45:10,540] [INFO] Running command: blastn -query GCF_014643375.1_ASM1464337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82efb94c-c692-4bbc-a8d3-b0871fbe3803/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643375.1_ASM1464337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:12,489] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:12,492] [INFO] Selected 16 target genomes.
[2024-01-25 18:45:12,492] [INFO] Target genome list was writen to GCF_014643375.1_ASM1464337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:12,508] [INFO] Task started: fastANI
[2024-01-25 18:45:12,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg47de5002-f4a6-424a-8e20-ef66e54143e8/GCF_014643375.1_ASM1464337v1_genomic.fna.gz --refList GCF_014643375.1_ASM1464337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643375.1_ASM1464337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:31,037] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:31,047] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:31,047] [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_014643375.1	s__Aureimonas_A glaciei	100.0	1861	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001425485.1	s__Aureimonas_A sp001425485	80.9976	913	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014380965.1	s__Aureimonas_A sp014380965	80.7593	443	1864	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_014196845.1	s__Aurantimonas endophytica	80.7156	810	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424685.1	s__Aureimonas_A sp001424685	80.6728	836	1864	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_001425575.1	s__Leaf443 sp001425575	80.5693	777	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	80.5004	764	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_010500835.1	s__Aurantimonas aggregata	80.4619	841	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	80.3423	748	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_014642635.1	s__Aureimonas_A endophytica	80.3251	790	1864	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_014196835.1	s__Aureimonas pseudogalii	80.2482	749	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893625.1	s__Mangrovicella endophytica	80.1564	736	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	80.0811	783	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	80.0751	725	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	78.1089	469	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	76.54	233	1864	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:31,049] [INFO] GTDB search result was written to GCF_014643375.1_ASM1464337v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:31,051] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:31,056] [INFO] DFAST_QC result json was written to GCF_014643375.1_ASM1464337v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:31,056] [INFO] DFAST_QC completed!
[2024-01-25 18:45:31,057] [INFO] Total running time: 0h1m41s