[2023-06-19 01:24:29,769] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:24:29,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:24:29,772] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference
[2023-06-19 01:24:31,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:24:31,243] [INFO] Task started: Prodigal
[2023-06-19 01:24:31,244] [INFO] Running command: gunzip -c /var/lib/cwl/stgba04395d-9542-46c0-b08f-62531973773a/GCA_018265755.1_ASM1826575v1_genomic.fna.gz | prodigal -d GCA_018265755.1_ASM1826575v1_genomic.fna/cds.fna -a GCA_018265755.1_ASM1826575v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:24:37,443] [INFO] Task succeeded: Prodigal
[2023-06-19 01:24:37,444] [INFO] Task started: HMMsearch
[2023-06-19 01:24:37,444] [INFO] Running command: hmmsearch --tblout GCA_018265755.1_ASM1826575v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/reference_markers.hmm GCA_018265755.1_ASM1826575v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:24:37,702] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:24:37,703] [INFO] Found 6/6 markers.
[2023-06-19 01:24:37,728] [INFO] Query marker FASTA was written to GCA_018265755.1_ASM1826575v1_genomic.fna/markers.fasta
[2023-06-19 01:24:37,729] [INFO] Task started: Blastn
[2023-06-19 01:24:37,729] [INFO] Running command: blastn -query GCA_018265755.1_ASM1826575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/reference_markers.fasta -out GCA_018265755.1_ASM1826575v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:24:38,481] [INFO] Task succeeded: Blastn
[2023-06-19 01:24:38,487] [INFO] Selected 27 target genomes.
[2023-06-19 01:24:38,488] [INFO] Target genome list was writen to GCA_018265755.1_ASM1826575v1_genomic.fna/target_genomes.txt
[2023-06-19 01:24:38,495] [INFO] Task started: fastANI
[2023-06-19 01:24:38,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgba04395d-9542-46c0-b08f-62531973773a/GCA_018265755.1_ASM1826575v1_genomic.fna.gz --refList GCA_018265755.1_ASM1826575v1_genomic.fna/target_genomes.txt --output GCA_018265755.1_ASM1826575v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:24:58,192] [INFO] Task succeeded: fastANI
[2023-06-19 01:24:58,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:24:58,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:24:58,214] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:24:58,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:24:58,215] [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	79.6235	284	727	95	below_threshold
Sutterella parvirubra	strain=YIT 11816	GCA_000250875.1	437898	437898	type	True	79.4472	281	727	95	below_threshold
Sutterella faecalis	strain=KGMB03119	GCA_006337085.1	2584944	2584944	type	True	78.6136	209	727	95	below_threshold
Sutterella wadsworthensis	strain=FDAARGOS_1159	GCA_016724805.1	40545	40545	type	True	77.6731	130	727	95	below_threshold
Sutterella wadsworthensis	strain=DSM 14016	GCA_003315195.1	40545	40545	type	True	77.6625	133	727	95	below_threshold
Duodenibacillus massiliensis	strain=Marseille-P2968	GCA_900128485.1	1852381	1852381	type	True	77.567	91	727	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.5937	73	727	95	below_threshold
Burkholderia gladioli	strain=NCTC12378	GCA_900446225.1	28095	28095	type	True	76.2085	85	727	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	76.1876	86	727	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	76.1585	86	727	95	below_threshold
Paraburkholderia lycopersici	strain=TNe-862	GCA_900096975.1	416944	416944	type	True	76.1233	80	727	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	76.1037	70	727	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	76.0954	54	727	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	76.0647	55	727	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_177	GCA_001525545.2	519	519	suspected-type	True	76.0499	54	727	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	75.9301	93	727	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	75.8055	66	727	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	75.7745	59	727	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	75.7467	58	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:24:58,219] [INFO] DFAST Taxonomy check result was written to GCA_018265755.1_ASM1826575v1_genomic.fna/tc_result.tsv
[2023-06-19 01:24:58,220] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:24:58,220] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:24:58,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/checkm_data
[2023-06-19 01:24:58,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:24:58,255] [INFO] Task started: CheckM
[2023-06-19 01:24:58,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018265755.1_ASM1826575v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018265755.1_ASM1826575v1_genomic.fna/checkm_input GCA_018265755.1_ASM1826575v1_genomic.fna/checkm_result
[2023-06-19 01:25:22,729] [INFO] Task succeeded: CheckM
[2023-06-19 01:25:22,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:25:22,764] [INFO] ===== Completeness check finished =====
[2023-06-19 01:25:22,765] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:25:22,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018265755.1_ASM1826575v1_genomic.fna/markers.fasta)
[2023-06-19 01:25:22,766] [INFO] Task started: Blastn
[2023-06-19 01:25:22,766] [INFO] Running command: blastn -query GCA_018265755.1_ASM1826575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4f71dce-56eb-4882-b955-4fb48901582a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018265755.1_ASM1826575v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:25:23,969] [INFO] Task succeeded: Blastn
[2023-06-19 01:25:23,973] [INFO] Selected 11 target genomes.
[2023-06-19 01:25:23,974] [INFO] Target genome list was writen to GCA_018265755.1_ASM1826575v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:25:23,979] [INFO] Task started: fastANI
[2023-06-19 01:25:23,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgba04395d-9542-46c0-b08f-62531973773a/GCA_018265755.1_ASM1826575v1_genomic.fna.gz --refList GCA_018265755.1_ASM1826575v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018265755.1_ASM1826575v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:25:29,053] [INFO] Task succeeded: fastANI
[2023-06-19 01:25:29,074] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:25:29,075] [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	98.704	667	727	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	86.5877	449	727	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	80.6823	286	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215795.1	s__Sutterella sp905215795	79.7477	221	727	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	79.6595	256	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	98.47	98.47	0.94	0.94	2	-
GCF_003609995.1	s__Sutterella megalosphaeroides	79.6053	285	727	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	79.5227	287	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250875.1	s__Sutterella parvirubra	79.4178	283	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	99.34	98.52	0.95	0.91	4	-
GCA_905186105.1	s__Sutterella sp905186105	79.3255	158	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sutterella	95.0	97.95	97.93	0.89	0.89	3	-
GCA_905202595.1	s__Sutterella sp905202595	78.4814	222	727	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	78.1616	153	727	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 01:25:29,081] [INFO] GTDB search result was written to GCA_018265755.1_ASM1826575v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:25:29,082] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:25:29,088] [INFO] DFAST_QC result json was written to GCA_018265755.1_ASM1826575v1_genomic.fna/dqc_result.json
[2023-06-19 01:25:29,089] [INFO] DFAST_QC completed!
[2023-06-19 01:25:29,089] [INFO] Total running time: 0h0m59s