[2024-01-25 17:53:05,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:05,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:05,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference
[2024-01-25 17:53:06,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:06,888] [INFO] Task started: Prodigal
[2024-01-25 17:53:06,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbbdbcf9-6d5e-4750-92c3-c6b88813c363/GCF_014058705.1_ASM1405870v1_genomic.fna.gz | prodigal -d GCF_014058705.1_ASM1405870v1_genomic.fna/cds.fna -a GCF_014058705.1_ASM1405870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:15,906] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:15,906] [INFO] Task started: HMMsearch
[2024-01-25 17:53:15,907] [INFO] Running command: hmmsearch --tblout GCF_014058705.1_ASM1405870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/reference_markers.hmm GCF_014058705.1_ASM1405870v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:16,103] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:16,103] [INFO] Found 6/6 markers.
[2024-01-25 17:53:16,131] [INFO] Query marker FASTA was written to GCF_014058705.1_ASM1405870v1_genomic.fna/markers.fasta
[2024-01-25 17:53:16,131] [INFO] Task started: Blastn
[2024-01-25 17:53:16,131] [INFO] Running command: blastn -query GCF_014058705.1_ASM1405870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/reference_markers.fasta -out GCF_014058705.1_ASM1405870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:17,151] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:17,153] [INFO] Selected 18 target genomes.
[2024-01-25 17:53:17,154] [INFO] Target genome list was writen to GCF_014058705.1_ASM1405870v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:17,161] [INFO] Task started: fastANI
[2024-01-25 17:53:17,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbdbcf9-6d5e-4750-92c3-c6b88813c363/GCF_014058705.1_ASM1405870v1_genomic.fna.gz --refList GCF_014058705.1_ASM1405870v1_genomic.fna/target_genomes.txt --output GCF_014058705.1_ASM1405870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:34,195] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:34,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:34,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:34,207] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:34,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:34,207] [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 mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	100.0	1161	1161	95	conclusive
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	81.4727	663	1161	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	80.2992	594	1161	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	80.2377	573	1161	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	80.1776	587	1161	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	80.1536	592	1161	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	80.1291	574	1161	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.6896	526	1161	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	79.5972	533	1161	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	79.4992	522	1161	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.3768	552	1161	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.3214	505	1161	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.1794	485	1161	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.6232	395	1161	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.3782	413	1161	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	78.2022	308	1161	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.886	317	1161	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	77.6293	241	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:34,208] [INFO] DFAST Taxonomy check result was written to GCF_014058705.1_ASM1405870v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:34,209] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:34,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:34,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/checkm_data
[2024-01-25 17:53:34,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:34,246] [INFO] Task started: CheckM
[2024-01-25 17:53:34,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014058705.1_ASM1405870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014058705.1_ASM1405870v1_genomic.fna/checkm_input GCF_014058705.1_ASM1405870v1_genomic.fna/checkm_result
[2024-01-25 17:54:04,261] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:04,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:04,280] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:04,280] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:04,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014058705.1_ASM1405870v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:04,281] [INFO] Task started: Blastn
[2024-01-25 17:54:04,281] [INFO] Running command: blastn -query GCF_014058705.1_ASM1405870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg042459c2-dfe0-4557-9ec3-84738eb0f1e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014058705.1_ASM1405870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:06,427] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:06,429] [INFO] Selected 17 target genomes.
[2024-01-25 17:54:06,429] [INFO] Target genome list was writen to GCF_014058705.1_ASM1405870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:06,443] [INFO] Task started: fastANI
[2024-01-25 17:54:06,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbbdbcf9-6d5e-4750-92c3-c6b88813c363/GCF_014058705.1_ASM1405870v1_genomic.fna.gz --refList GCF_014058705.1_ASM1405870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014058705.1_ASM1405870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:22,308] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:22,319] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:22,319] [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_014058705.1	s__Aureimonas mangrovi	100.0	1161	1161	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_017815515.1	s__Aureimonas populi	81.4967	662	1161	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	80.293	595	1161	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	80.2753	556	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423245.1	s__Aureimonas sp001423245	80.2603	569	1161	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	80.2578	572	1161	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	80.1575	589	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001425575.1	s__Leaf443 sp001425575	80.1518	572	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	80.0778	581	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001463765.1	s__Aureimonas sp001463765	80.07	532	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	80.0014	578	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765365.1	s__VTOM01 sp009765365	79.6841	571	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	79.5805	513	1161	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	79.5773	536	1161	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_000421645.1	s__Aurantimonas coralicida	79.5032	520	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_010500815.1	s__Jiella pacifica	79.2185	481	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	79.1718	522	1161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:22,320] [INFO] GTDB search result was written to GCF_014058705.1_ASM1405870v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:22,321] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:22,324] [INFO] DFAST_QC result json was written to GCF_014058705.1_ASM1405870v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:22,325] [INFO] DFAST_QC completed!
[2024-01-25 17:54:22,325] [INFO] Total running time: 0h1m17s