[2024-01-24 14:53:50,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference
[2024-01-24 14:53:51,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,544] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be1788e-f6e3-4b98-ae8b-af5a5f3959b9/GCF_017183135.1_ASM1718313v1_genomic.fna.gz | prodigal -d GCF_017183135.1_ASM1718313v1_genomic.fna/cds.fna -a GCF_017183135.1_ASM1718313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:02,824] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:02,824] [INFO] Task started: HMMsearch
[2024-01-24 14:54:02,825] [INFO] Running command: hmmsearch --tblout GCF_017183135.1_ASM1718313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/reference_markers.hmm GCF_017183135.1_ASM1718313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:03,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:03,112] [INFO] Found 6/6 markers.
[2024-01-24 14:54:03,159] [INFO] Query marker FASTA was written to GCF_017183135.1_ASM1718313v1_genomic.fna/markers.fasta
[2024-01-24 14:54:03,160] [INFO] Task started: Blastn
[2024-01-24 14:54:03,160] [INFO] Running command: blastn -query GCF_017183135.1_ASM1718313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/reference_markers.fasta -out GCF_017183135.1_ASM1718313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:04,206] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:04,209] [INFO] Selected 12 target genomes.
[2024-01-24 14:54:04,210] [INFO] Target genome list was writen to GCF_017183135.1_ASM1718313v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:04,230] [INFO] Task started: fastANI
[2024-01-24 14:54:04,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be1788e-f6e3-4b98-ae8b-af5a5f3959b9/GCF_017183135.1_ASM1718313v1_genomic.fna.gz --refList GCF_017183135.1_ASM1718313v1_genomic.fna/target_genomes.txt --output GCF_017183135.1_ASM1718313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:15,536] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:15,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:15,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:15,551] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:15,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:15,552] [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 marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	100.0	1309	1314	95	conclusive
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	81.4645	765	1314	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	81.4251	768	1314	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	81.3933	790	1314	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	81.2895	796	1314	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.8863	726	1314	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.6683	732	1314	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.6328	749	1314	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.8869	623	1314	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	78.3357	430	1314	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.6485	356	1314	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.2311	288	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:15,554] [INFO] DFAST Taxonomy check result was written to GCF_017183135.1_ASM1718313v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:15,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:15,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:15,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/checkm_data
[2024-01-24 14:54:15,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:15,598] [INFO] Task started: CheckM
[2024-01-24 14:54:15,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017183135.1_ASM1718313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017183135.1_ASM1718313v1_genomic.fna/checkm_input GCF_017183135.1_ASM1718313v1_genomic.fna/checkm_result
[2024-01-24 14:54:51,242] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:51,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:51,263] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:51,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:51,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017183135.1_ASM1718313v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:51,265] [INFO] Task started: Blastn
[2024-01-24 14:54:51,265] [INFO] Running command: blastn -query GCF_017183135.1_ASM1718313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dd1b41c-8c53-4fc5-a927-12666ae15a6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017183135.1_ASM1718313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:53,154] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:53,159] [INFO] Selected 10 target genomes.
[2024-01-24 14:54:53,159] [INFO] Target genome list was writen to GCF_017183135.1_ASM1718313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:53,172] [INFO] Task started: fastANI
[2024-01-24 14:54:53,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be1788e-f6e3-4b98-ae8b-af5a5f3959b9/GCF_017183135.1_ASM1718313v1_genomic.fna.gz --refList GCF_017183135.1_ASM1718313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017183135.1_ASM1718313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:03,476] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:03,488] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:03,488] [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_017183135.1	s__Aurantimonas sp017183135	100.0	1309	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011050685.1	s__Aurantimonas coralicida_A	90.4917	1079	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_000153465.1	s__Aurantimonas manganoxydans	81.4556	766	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_000421645.1	s__Aurantimonas coralicida	81.3983	790	1314	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	80.8773	728	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	80.6656	733	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	79.8754	625	1314	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	79.7222	662	1314	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	79.7026	623	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	78.3407	430	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:03,490] [INFO] GTDB search result was written to GCF_017183135.1_ASM1718313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:03,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:03,493] [INFO] DFAST_QC result json was written to GCF_017183135.1_ASM1718313v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:03,494] [INFO] DFAST_QC completed!
[2024-01-24 14:55:03,494] [INFO] Total running time: 0h1m13s