[2024-01-24 14:11:47,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:47,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:47,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference
[2024-01-24 14:11:49,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:49,178] [INFO] Task started: Prodigal
[2024-01-24 14:11:49,178] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1bafaaf-3ed0-4bce-b207-a9c38f612354/GCF_000421645.1_ASM42164v1_genomic.fna.gz | prodigal -d GCF_000421645.1_ASM42164v1_genomic.fna/cds.fna -a GCF_000421645.1_ASM42164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:02,824] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:02,824] [INFO] Task started: HMMsearch
[2024-01-24 14:12:02,824] [INFO] Running command: hmmsearch --tblout GCF_000421645.1_ASM42164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/reference_markers.hmm GCF_000421645.1_ASM42164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:03,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:03,231] [INFO] Found 6/6 markers.
[2024-01-24 14:12:03,276] [INFO] Query marker FASTA was written to GCF_000421645.1_ASM42164v1_genomic.fna/markers.fasta
[2024-01-24 14:12:03,277] [INFO] Task started: Blastn
[2024-01-24 14:12:03,277] [INFO] Running command: blastn -query GCF_000421645.1_ASM42164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/reference_markers.fasta -out GCF_000421645.1_ASM42164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:05,454] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:05,459] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:05,459] [INFO] Target genome list was writen to GCF_000421645.1_ASM42164v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:05,465] [INFO] Task started: fastANI
[2024-01-24 14:12:05,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1bafaaf-3ed0-4bce-b207-a9c38f612354/GCF_000421645.1_ASM42164v1_genomic.fna.gz --refList GCF_000421645.1_ASM42164v1_genomic.fna/target_genomes.txt --output GCF_000421645.1_ASM42164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:17,641] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:17,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:17,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:17,674] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:12:17,674] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:12:17,675] [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 coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	100.0	1515	1517	95	inconclusive
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	99.9753	1482	1517	95	inconclusive
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	95.3885	1249	1517	95	inconclusive
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	95.3668	1282	1517	95	inconclusive
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	82.5219	900	1517	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	82.272	892	1517	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	81.339	798	1517	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	81.0406	799	1517	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.2212	442	1517	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.095	380	1517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:17,676] [INFO] DFAST Taxonomy check result was written to GCF_000421645.1_ASM42164v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:17,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:17,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:17,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/checkm_data
[2024-01-24 14:12:17,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:17,727] [INFO] Task started: CheckM
[2024-01-24 14:12:17,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421645.1_ASM42164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421645.1_ASM42164v1_genomic.fna/checkm_input GCF_000421645.1_ASM42164v1_genomic.fna/checkm_result
[2024-01-24 14:13:03,690] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:03,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,715] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:03,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:03,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421645.1_ASM42164v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:03,717] [INFO] Task started: Blastn
[2024-01-24 14:13:03,717] [INFO] Running command: blastn -query GCF_000421645.1_ASM42164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2671d435-3cd6-4ed9-b3e8-20eed62c1d76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421645.1_ASM42164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:06,040] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:06,043] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:06,043] [INFO] Target genome list was writen to GCF_000421645.1_ASM42164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:06,052] [INFO] Task started: fastANI
[2024-01-24 14:13:06,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1bafaaf-3ed0-4bce-b207-a9c38f612354/GCF_000421645.1_ASM42164v1_genomic.fna.gz --refList GCF_000421645.1_ASM42164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421645.1_ASM42164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:16,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:16,912] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:16,912] [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_000421645.1	s__Aurantimonas coralicida	100.0	1515	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	conclusive
GCF_000153465.1	s__Aurantimonas manganoxydans	95.3668	1282	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_010500835.1	s__Aurantimonas aggregata	82.5307	899	1517	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	82.2677	905	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	81.8951	860	1517	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	81.5808	854	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050685.1	s__Aurantimonas coralicida_A	81.3763	796	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	-
GCF_017183135.1	s__Aurantimonas sp017183135	81.3288	800	1517	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	81.0019	805	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425575.1	s__Leaf443 sp001425575	80.6288	714	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:16,914] [INFO] GTDB search result was written to GCF_000421645.1_ASM42164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:16,915] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:16,917] [INFO] DFAST_QC result json was written to GCF_000421645.1_ASM42164v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:16,918] [INFO] DFAST_QC completed!
[2024-01-24 14:13:16,918] [INFO] Total running time: 0h1m29s