[2024-01-24 14:47:19,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference
[2024-01-24 14:47:21,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,078] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,078] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa5045ff-7cf9-4137-9f60-18d5c6d4d974/GCF_010994455.1_ASM1099445v2_genomic.fna.gz | prodigal -d GCF_010994455.1_ASM1099445v2_genomic.fna/cds.fna -a GCF_010994455.1_ASM1099445v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:39,165] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:39,165] [INFO] Task started: HMMsearch
[2024-01-24 14:47:39,165] [INFO] Running command: hmmsearch --tblout GCF_010994455.1_ASM1099445v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/reference_markers.hmm GCF_010994455.1_ASM1099445v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:39,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:39,535] [INFO] Found 6/6 markers.
[2024-01-24 14:47:39,593] [INFO] Query marker FASTA was written to GCF_010994455.1_ASM1099445v2_genomic.fna/markers.fasta
[2024-01-24 14:47:39,593] [INFO] Task started: Blastn
[2024-01-24 14:47:39,594] [INFO] Running command: blastn -query GCF_010994455.1_ASM1099445v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/reference_markers.fasta -out GCF_010994455.1_ASM1099445v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:40,760] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:40,771] [INFO] Selected 9 target genomes.
[2024-01-24 14:47:40,771] [INFO] Target genome list was writen to GCF_010994455.1_ASM1099445v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:41,125] [INFO] Task started: fastANI
[2024-01-24 14:47:41,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa5045ff-7cf9-4137-9f60-18d5c6d4d974/GCF_010994455.1_ASM1099445v2_genomic.fna.gz --refList GCF_010994455.1_ASM1099445v2_genomic.fna/target_genomes.txt --output GCF_010994455.1_ASM1099445v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:55,383] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:55,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:55,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:55,393] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:55,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:55,394] [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
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	99.9991	2006	2007	95	conclusive
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	86.757	1105	2007	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	86.6846	1125	2007	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	86.6743	1336	2007	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	86.5913	1365	2007	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	86.347	1367	2007	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	85.9049	1190	2007	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	85.5102	1130	2007	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	85.4588	1138	2007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:55,397] [INFO] DFAST Taxonomy check result was written to GCF_010994455.1_ASM1099445v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:55,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:55,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:55,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/checkm_data
[2024-01-24 14:47:55,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:55,470] [INFO] Task started: CheckM
[2024-01-24 14:47:55,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010994455.1_ASM1099445v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010994455.1_ASM1099445v2_genomic.fna/checkm_input GCF_010994455.1_ASM1099445v2_genomic.fna/checkm_result
[2024-01-24 14:48:51,586] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:51,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:51,609] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:51,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:51,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010994455.1_ASM1099445v2_genomic.fna/markers.fasta)
[2024-01-24 14:48:51,611] [INFO] Task started: Blastn
[2024-01-24 14:48:51,611] [INFO] Running command: blastn -query GCF_010994455.1_ASM1099445v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39ee99a-70cd-4594-bb49-fe8e36e10c30/dqc_reference/reference_markers_gtdb.fasta -out GCF_010994455.1_ASM1099445v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:54,113] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:54,117] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:54,117] [INFO] Target genome list was writen to GCF_010994455.1_ASM1099445v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:54,137] [INFO] Task started: fastANI
[2024-01-24 14:48:54,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa5045ff-7cf9-4137-9f60-18d5c6d4d974/GCF_010994455.1_ASM1099445v2_genomic.fna.gz --refList GCF_010994455.1_ASM1099445v2_genomic.fna/target_genomes_gtdb.txt --output GCF_010994455.1_ASM1099445v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:09,918] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:09,934] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:49:09,935] [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_003432075.1	s__Shinella sp003432075	90.136	1451	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	86.7606	1105	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	86.6955	1332	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_003574625.1	s__Shinella zoogloeoides_A	86.4276	1223	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827055.1	s__Shinella kummerowiae	86.3254	1370	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	86.2725	1204	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713395.1	s__Shinella sp001713395	86.0384	1386	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	85.9257	1187	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262505.1	s__Shinella sp001262505	85.9194	1364	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_004514435.1	s__Shinella sp004514435	85.6079	1112	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCA_002364745.1	s__Shinella sp002364745	84.8278	1092	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.33	99.33	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:09,937] [INFO] GTDB search result was written to GCF_010994455.1_ASM1099445v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:09,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:09,941] [INFO] DFAST_QC result json was written to GCF_010994455.1_ASM1099445v2_genomic.fna/dqc_result.json
[2024-01-24 14:49:09,941] [INFO] DFAST_QC completed!
[2024-01-24 14:49:09,941] [INFO] Total running time: 0h1m50s