[2023-06-19 08:29:35,443] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:29:35,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:29:35,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference
[2023-06-19 08:29:37,621] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:29:37,622] [INFO] Task started: Prodigal
[2023-06-19 08:29:37,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg981371fe-11ff-4d08-8b9f-cf12c4f00575/GCA_018377975.1_ASM1837797v1_genomic.fna.gz | prodigal -d GCA_018377975.1_ASM1837797v1_genomic.fna/cds.fna -a GCA_018377975.1_ASM1837797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:29:43,657] [INFO] Task succeeded: Prodigal
[2023-06-19 08:29:43,658] [INFO] Task started: HMMsearch
[2023-06-19 08:29:43,658] [INFO] Running command: hmmsearch --tblout GCA_018377975.1_ASM1837797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/reference_markers.hmm GCA_018377975.1_ASM1837797v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:29:43,902] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:29:43,903] [INFO] Found 6/6 markers.
[2023-06-19 08:29:43,938] [INFO] Query marker FASTA was written to GCA_018377975.1_ASM1837797v1_genomic.fna/markers.fasta
[2023-06-19 08:29:43,938] [INFO] Task started: Blastn
[2023-06-19 08:29:43,939] [INFO] Running command: blastn -query GCA_018377975.1_ASM1837797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/reference_markers.fasta -out GCA_018377975.1_ASM1837797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:44,743] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:44,749] [INFO] Selected 26 target genomes.
[2023-06-19 08:29:44,749] [INFO] Target genome list was writen to GCA_018377975.1_ASM1837797v1_genomic.fna/target_genomes.txt
[2023-06-19 08:29:44,752] [INFO] Task started: fastANI
[2023-06-19 08:29:44,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg981371fe-11ff-4d08-8b9f-cf12c4f00575/GCA_018377975.1_ASM1837797v1_genomic.fna.gz --refList GCA_018377975.1_ASM1837797v1_genomic.fna/target_genomes.txt --output GCA_018377975.1_ASM1837797v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:30:03,708] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:03,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:30:03,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:30:03,735] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:30:03,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:30:03,736] [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
Sutterella megalosphaeroides	strain=6FBBBH3	GCA_003609995.1	2494234	2494234	type	True	79.801	271	654	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	79.6346	258	654	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.9313	217	654	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.9373	122	654	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	77.9343	124	654	95	below_threshold
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	77.4082	93	654	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.8783	72	654	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	76.6281	51	654	95	below_threshold
Burkholderia gladioli	strain=NCTC12378	GCA_900446225.1	28095	28095	type	True	76.5158	86	654	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	76.4693	85	654	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	76.4293	87	654	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	76.3157	72	654	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	76.2163	91	654	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	76.0804	59	654	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.0292	72	654	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	75.9757	93	654	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	75.8554	67	654	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:30:03,739] [INFO] DFAST Taxonomy check result was written to GCA_018377975.1_ASM1837797v1_genomic.fna/tc_result.tsv
[2023-06-19 08:30:03,739] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:30:03,740] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:30:03,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/checkm_data
[2023-06-19 08:30:03,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:30:03,774] [INFO] Task started: CheckM
[2023-06-19 08:30:03,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018377975.1_ASM1837797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018377975.1_ASM1837797v1_genomic.fna/checkm_input GCA_018377975.1_ASM1837797v1_genomic.fna/checkm_result
[2023-06-19 08:30:27,989] [INFO] Task succeeded: CheckM
[2023-06-19 08:30:27,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:30:28,016] [INFO] ===== Completeness check finished =====
[2023-06-19 08:30:28,017] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:30:28,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018377975.1_ASM1837797v1_genomic.fna/markers.fasta)
[2023-06-19 08:30:28,018] [INFO] Task started: Blastn
[2023-06-19 08:30:28,018] [INFO] Running command: blastn -query GCA_018377975.1_ASM1837797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg817abba2-4d11-4364-aa38-933b87b8c709/dqc_reference/reference_markers_gtdb.fasta -out GCA_018377975.1_ASM1837797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:30:29,319] [INFO] Task succeeded: Blastn
[2023-06-19 08:30:29,326] [INFO] Selected 11 target genomes.
[2023-06-19 08:30:29,327] [INFO] Target genome list was writen to GCA_018377975.1_ASM1837797v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:30:29,328] [INFO] Task started: fastANI
[2023-06-19 08:30:29,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg981371fe-11ff-4d08-8b9f-cf12c4f00575/GCA_018377975.1_ASM1837797v1_genomic.fna.gz --refList GCA_018377975.1_ASM1837797v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018377975.1_ASM1837797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:30:34,503] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:34,524] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:30:34,524] [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_000297775.1	s__Sutterella wadsworthensis_A	98.7346	587	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.94	98.60	0.92	0.86	8	conclusive
GCA_900764215.1	s__Sutterella sp900764215	87.2244	441	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.09	99.09	0.76	0.76	2	-
GCA_017936545.1	s__Sutterella sp017936545	80.673	262	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905186105.1	s__Sutterella sp905186105	80.0798	141	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	97.95	97.93	0.89	0.89	3	-
GCA_905215795.1	s__Sutterella sp905215795	80.0086	215	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609995.1	s__Sutterella megalosphaeroides	79.821	270	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198475.1	s__Sutterella sp905198475	79.8142	271	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754475.1	s__Sutterella sp900754475	79.7342	249	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.47	98.47	0.94	0.94	2	-
GCF_000250875.1	s__Sutterella parvirubra	79.6546	257	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.34	98.52	0.95	0.91	4	-
GCA_905202595.1	s__Sutterella sp905202595	78.8336	195	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905194315.1	s__Sutterella sp905194315	77.9258	140	654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:30:34,527] [INFO] GTDB search result was written to GCA_018377975.1_ASM1837797v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:30:34,528] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:30:34,535] [INFO] DFAST_QC result json was written to GCA_018377975.1_ASM1837797v1_genomic.fna/dqc_result.json
[2023-06-19 08:30:34,536] [INFO] DFAST_QC completed!
[2023-06-19 08:30:34,536] [INFO] Total running time: 0h0m59s