[2024-01-24 13:12:56,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,132] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference
[2024-01-24 13:12:57,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,543] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg423487c3-3f96-49e2-9c08-c20ea2725575/GCF_004519335.1_ASM451933v1_genomic.fna.gz | prodigal -d GCF_004519335.1_ASM451933v1_genomic.fna/cds.fna -a GCF_004519335.1_ASM451933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:12,246] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:12,247] [INFO] Task started: HMMsearch
[2024-01-24 13:13:12,247] [INFO] Running command: hmmsearch --tblout GCF_004519335.1_ASM451933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/reference_markers.hmm GCF_004519335.1_ASM451933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:12,574] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:12,575] [INFO] Found 6/6 markers.
[2024-01-24 13:13:12,624] [INFO] Query marker FASTA was written to GCF_004519335.1_ASM451933v1_genomic.fna/markers.fasta
[2024-01-24 13:13:12,625] [INFO] Task started: Blastn
[2024-01-24 13:13:12,625] [INFO] Running command: blastn -query GCF_004519335.1_ASM451933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/reference_markers.fasta -out GCF_004519335.1_ASM451933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:13,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:13,740] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:13,741] [INFO] Target genome list was writen to GCF_004519335.1_ASM451933v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:13,753] [INFO] Task started: fastANI
[2024-01-24 13:13:13,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg423487c3-3f96-49e2-9c08-c20ea2725575/GCF_004519335.1_ASM451933v1_genomic.fna.gz --refList GCF_004519335.1_ASM451933v1_genomic.fna/target_genomes.txt --output GCF_004519335.1_ASM451933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:31,788] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:31,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:31,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:31,802] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:31,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:31,803] [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
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	100.0	1715	1737	95	conclusive
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	85.0254	1211	1737	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	84.348	1172	1737	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	81.1779	801	1737	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	81.1244	796	1737	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	81.1237	805	1737	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	81.0781	779	1737	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	81.0194	767	1737	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.9222	809	1737	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.8235	813	1737	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.7009	652	1737	95	below_threshold
Fulvimarina endophytica	strain=85	GCA_003403015.1	2293836	2293836	type	True	79.6032	605	1737	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	79.0138	566	1737	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.4139	551	1737	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.0781	502	1737	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.7378	401	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:31,804] [INFO] DFAST Taxonomy check result was written to GCF_004519335.1_ASM451933v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:31,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:31,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:31,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/checkm_data
[2024-01-24 13:13:31,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:31,861] [INFO] Task started: CheckM
[2024-01-24 13:13:31,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004519335.1_ASM451933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004519335.1_ASM451933v1_genomic.fna/checkm_input GCF_004519335.1_ASM451933v1_genomic.fna/checkm_result
[2024-01-24 13:14:18,463] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:18,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 20.83%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,504] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:18,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:18,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004519335.1_ASM451933v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:18,505] [INFO] Task started: Blastn
[2024-01-24 13:14:18,505] [INFO] Running command: blastn -query GCF_004519335.1_ASM451933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b05f36-877c-4d60-bc3c-66e58fa08e71/dqc_reference/reference_markers_gtdb.fasta -out GCF_004519335.1_ASM451933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:20,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:20,628] [INFO] Selected 9 target genomes.
[2024-01-24 13:14:20,628] [INFO] Target genome list was writen to GCF_004519335.1_ASM451933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:20,639] [INFO] Task started: fastANI
[2024-01-24 13:14:20,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg423487c3-3f96-49e2-9c08-c20ea2725575/GCF_004519335.1_ASM451933v1_genomic.fna.gz --refList GCF_004519335.1_ASM451933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004519335.1_ASM451933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:33,544] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:33,557] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:33,557] [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_004519335.1	s__Jiella endophytica	100.0	1709	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002088275.1	s__Jiella sp002088275	85.3079	1212	1737	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	84.9979	1214	1737	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	84.9552	1211	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	84.3469	1172	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	83.9305	1112	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	81.077	761	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	79.0778	603	1737	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	78.6704	552	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	98.47	96.94	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,559] [INFO] GTDB search result was written to GCF_004519335.1_ASM451933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:33,559] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:33,563] [INFO] DFAST_QC result json was written to GCF_004519335.1_ASM451933v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:33,563] [INFO] DFAST_QC completed!
[2024-01-24 13:14:33,563] [INFO] Total running time: 0h1m37s