[2024-01-25 19:07:35,432] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference
[2024-01-25 19:07:36,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,574] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,575] [INFO] Running command: gunzip -c /var/lib/cwl/stgd10d77e1-46ce-4c25-a600-c4e86e177d23/GCF_017815135.1_ASM1781513v1_genomic.fna.gz | prodigal -d GCF_017815135.1_ASM1781513v1_genomic.fna/cds.fna -a GCF_017815135.1_ASM1781513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:48,517] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:48,518] [INFO] Task started: HMMsearch
[2024-01-25 19:07:48,518] [INFO] Running command: hmmsearch --tblout GCF_017815135.1_ASM1781513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/reference_markers.hmm GCF_017815135.1_ASM1781513v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:48,815] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:48,815] [INFO] Found 6/6 markers.
[2024-01-25 19:07:48,859] [INFO] Query marker FASTA was written to GCF_017815135.1_ASM1781513v1_genomic.fna/markers.fasta
[2024-01-25 19:07:48,859] [INFO] Task started: Blastn
[2024-01-25 19:07:48,859] [INFO] Running command: blastn -query GCF_017815135.1_ASM1781513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/reference_markers.fasta -out GCF_017815135.1_ASM1781513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:49,919] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:49,922] [INFO] Selected 15 target genomes.
[2024-01-25 19:07:49,922] [INFO] Target genome list was writen to GCF_017815135.1_ASM1781513v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:49,946] [INFO] Task started: fastANI
[2024-01-25 19:07:49,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10d77e1-46ce-4c25-a600-c4e86e177d23/GCF_017815135.1_ASM1781513v1_genomic.fna.gz --refList GCF_017815135.1_ASM1781513v1_genomic.fna/target_genomes.txt --output GCF_017815135.1_ASM1781513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:04,956] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:04,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:04,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:04,968] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:08:04,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:08:04,968] [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	83.8719	1118	1621	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	83.6792	1106	1621	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	83.3096	1072	1621	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	80.7501	721	1621	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.7212	702	1621	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.6557	729	1621	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	80.6173	745	1621	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.5463	706	1621	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.2257	728	1621	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.2199	725	1621	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.5931	606	1621	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	78.6819	520	1621	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.9158	385	1621	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	77.4973	369	1621	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.1747	372	1621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:04,970] [INFO] DFAST Taxonomy check result was written to GCF_017815135.1_ASM1781513v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:04,971] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:04,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:04,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/checkm_data
[2024-01-25 19:08:04,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:05,022] [INFO] Task started: CheckM
[2024-01-25 19:08:05,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017815135.1_ASM1781513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017815135.1_ASM1781513v1_genomic.fna/checkm_input GCF_017815135.1_ASM1781513v1_genomic.fna/checkm_result
[2024-01-25 19:08:43,586] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:43,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:43,606] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:43,607] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:43,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017815135.1_ASM1781513v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:43,607] [INFO] Task started: Blastn
[2024-01-25 19:08:43,607] [INFO] Running command: blastn -query GCF_017815135.1_ASM1781513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c18a6b0-d747-4745-b014-8a1a060402e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017815135.1_ASM1781513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:45,672] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:45,674] [INFO] Selected 7 target genomes.
[2024-01-25 19:08:45,675] [INFO] Target genome list was writen to GCF_017815135.1_ASM1781513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:45,683] [INFO] Task started: fastANI
[2024-01-25 19:08:45,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10d77e1-46ce-4c25-a600-c4e86e177d23/GCF_017815135.1_ASM1781513v1_genomic.fna.gz --refList GCF_017815135.1_ASM1781513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017815135.1_ASM1781513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:55,192] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:55,198] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:55,198] [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_017815135.1	s__Jiella sp017815135	100.0	1619	1621	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	84.1627	1123	1621	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	84.0528	1096	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	83.8831	1115	1621	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	83.7014	1103	1621	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	83.2891	1075	1621	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349315.1	s__Jiella sp017349315	81.3064	893	1621	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 19:08:55,200] [INFO] GTDB search result was written to GCF_017815135.1_ASM1781513v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:55,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:55,203] [INFO] DFAST_QC result json was written to GCF_017815135.1_ASM1781513v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:55,203] [INFO] DFAST_QC completed!
[2024-01-25 19:08:55,204] [INFO] Total running time: 0h1m20s