[2024-01-24 12:31:34,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference
[2024-01-24 12:31:35,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,587] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,587] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdf6bdcf-d55c-461d-9eff-869c08465403/GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna.gz | prodigal -d GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/cds.fna -a GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:41,967] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:41,967] [INFO] Task started: HMMsearch
[2024-01-24 12:31:41,967] [INFO] Running command: hmmsearch --tblout GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/reference_markers.hmm GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:42,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:42,248] [INFO] Found 6/6 markers.
[2024-01-24 12:31:42,293] [INFO] Query marker FASTA was written to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/markers.fasta
[2024-01-24 12:31:42,293] [INFO] Task started: Blastn
[2024-01-24 12:31:42,293] [INFO] Running command: blastn -query GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/reference_markers.fasta -out GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:43,074] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:43,079] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:43,080] [INFO] Target genome list was writen to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:43,087] [INFO] Task started: fastANI
[2024-01-24 12:31:43,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf6bdcf-d55c-461d-9eff-869c08465403/GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna.gz --refList GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:55,156] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:55,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:55,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:55,167] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:55,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:55,168] [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
Proteus myxofaciens	strain=ATCC 19692	GCA_001654855.1	184072	184072	type	True	100.0	1121	1126	95	conclusive
Proteus faecis	strain=TJ1636	GCA_003144395.1	2050967	2050967	type	True	82.9289	822	1126	95	below_threshold
Proteus columbae	strain=08MAS2615	GCA_002777965.1	1987580	1987580	type	True	82.9081	812	1126	95	below_threshold
Proteus alimentorum	strain=08MAS0041	GCA_002607735.1	1973495	1973495	type	True	82.8889	797	1126	95	below_threshold
Proteus terrae	strain=LMG 28659	GCA_003144325.1	1574161	1574161	type	True	82.8487	804	1126	95	below_threshold
Proteus cibi	strain=FJ2001126-3	GCA_003144405.1	2050966	2050966	type	True	82.7887	800	1126	95	below_threshold
Proteus terrae subsp. cibarius	strain=JCM 30699	GCA_003144495.1	626774	1574161	type	True	82.7661	809	1126	95	below_threshold
Proteus penneri	strain=FDAARGOS_874	GCA_016028675.1	102862	102862	type	True	82.748	804	1126	95	below_threshold
Proteus penneri	strain=NCTC12737	GCA_900455015.1	102862	102862	type	True	82.7279	800	1126	95	below_threshold
Proteus hauseri	strain=ATCC 700826	GCA_001654965.1	183417	183417	type	True	82.5444	792	1126	95	below_threshold
Proteus mirabilis	strain=ATCC 29906	GCA_000160755.1	584	584	type	True	82.3757	744	1126	95	below_threshold
Providencia manganoxydans	strain=LLDRA6	GCA_016618195.1	2923283	2923283	type	True	77.9209	260	1126	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	77.4978	96	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,169] [INFO] DFAST Taxonomy check result was written to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:55,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:55,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:55,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/checkm_data
[2024-01-24 12:31:55,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:55,213] [INFO] Task started: CheckM
[2024-01-24 12:31:55,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/checkm_input GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/checkm_result
[2024-01-24 12:32:20,615] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:20,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,638] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:20,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:20,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-24 12:32:20,639] [INFO] Task started: Blastn
[2024-01-24 12:32:20,639] [INFO] Running command: blastn -query GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16e32b9-3110-46d5-a5d3-58499ced8735/dqc_reference/reference_markers_gtdb.fasta -out GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:21,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:21,573] [INFO] Selected 15 target genomes.
[2024-01-24 12:32:21,573] [INFO] Target genome list was writen to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:21,585] [INFO] Task started: fastANI
[2024-01-24 12:32:21,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdf6bdcf-d55c-461d-9eff-869c08465403/GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna.gz --refList GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:33,680] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:33,696] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:33,697] [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_001654855.1	s__Proteus myxofaciens	100.0	1121	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011045835.1	s__Proteus cibarius	82.9525	804	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.79	96.76	0.92	0.88	25	-
GCF_009914335.1	s__Proteus sp003144505	82.9509	812	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.18	97.72	0.94	0.91	8	-
GCF_003144395.1	s__Proteus faecis	82.9187	823	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.18	98.84	0.96	0.95	3	-
GCF_002777965.1	s__Proteus columbae	82.9081	812	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144375.1	s__Proteus sp003144375	82.8993	817	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.93	98.24	0.92	0.92	3	-
GCF_014897315.1	s__Proteus sp014897315	82.8984	797	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045815.1	s__Proteus vulgaris_B	82.8477	833	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.83	98.17	0.95	0.93	4	-
GCF_003144325.1	s__Proteus terrae	82.8409	805	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	96.4726	98.30	96.81	0.93	0.92	6	-
GCF_016647575.1	s__Proteus mirabilis_B	82.8183	815	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.5013	98.84	97.67	0.96	0.91	3	-
GCF_003144405.1	s__Proteus cibi	82.7938	799	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.44	99.18	0.92	0.85	4	-
GCF_003144535.1	s__Proteus penneri	82.7508	807	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	99.41	98.65	0.95	0.93	24	-
GCF_001722135.1	s__Proteus sp001722135	82.6292	830	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	100.00	100.00	0.99	0.99	3	-
GCF_001654965.1	s__Proteus hauseri	82.5543	791	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.69	97.81	0.97	0.94	4	-
GCF_000160755.1	s__Proteus mirabilis	82.3757	744	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Proteus	95.0	98.92	96.50	0.93	0.87	405	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:33,698] [INFO] GTDB search result was written to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:33,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:33,703] [INFO] DFAST_QC result json was written to GCF_001654855.1_Cmy19692_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-24 12:32:33,703] [INFO] DFAST_QC completed!
[2024-01-24 12:32:33,703] [INFO] Total running time: 0h0m60s