[2024-01-24 12:36:50,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:50,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:50,189] [INFO] DQC Reference Directory: /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference
[2024-01-24 12:36:52,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:52,576] [INFO] Task started: Prodigal
[2024-01-24 12:36:52,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgad90837a-fc50-4a42-b07b-d3240fa7ee91/GCF_004514425.2_ASM451442v2_genomic.fna.gz | prodigal -d GCF_004514425.2_ASM451442v2_genomic.fna/cds.fna -a GCF_004514425.2_ASM451442v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:08,260] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:08,261] [INFO] Task started: HMMsearch
[2024-01-24 12:37:08,261] [INFO] Running command: hmmsearch --tblout GCF_004514425.2_ASM451442v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/reference_markers.hmm GCF_004514425.2_ASM451442v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:08,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:08,506] [INFO] Found 6/6 markers.
[2024-01-24 12:37:08,548] [INFO] Query marker FASTA was written to GCF_004514425.2_ASM451442v2_genomic.fna/markers.fasta
[2024-01-24 12:37:08,549] [INFO] Task started: Blastn
[2024-01-24 12:37:08,549] [INFO] Running command: blastn -query GCF_004514425.2_ASM451442v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/reference_markers.fasta -out GCF_004514425.2_ASM451442v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:09,437] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:09,441] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:09,441] [INFO] Target genome list was writen to GCF_004514425.2_ASM451442v2_genomic.fna/target_genomes.txt
[2024-01-24 12:37:09,466] [INFO] Task started: fastANI
[2024-01-24 12:37:09,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgad90837a-fc50-4a42-b07b-d3240fa7ee91/GCF_004514425.2_ASM451442v2_genomic.fna.gz --refList GCF_004514425.2_ASM451442v2_genomic.fna/target_genomes.txt --output GCF_004514425.2_ASM451442v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:21,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:21,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:21,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:21,810] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:21,810] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:37:21,810] [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 sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	100.0	1762	1766	95	inconclusive
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	96.5634	1501	1766	95	inconclusive
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	86.4605	1021	1766	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	86.4422	1013	1766	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	86.0393	1056	1766	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	85.9949	1161	1766	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	85.9888	1170	1766	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	85.5807	1111	1766	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	85.2352	1169	1766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:21,812] [INFO] DFAST Taxonomy check result was written to GCF_004514425.2_ASM451442v2_genomic.fna/tc_result.tsv
[2024-01-24 12:37:21,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:21,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:21,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/checkm_data
[2024-01-24 12:37:21,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:21,861] [INFO] Task started: CheckM
[2024-01-24 12:37:21,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004514425.2_ASM451442v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004514425.2_ASM451442v2_genomic.fna/checkm_input GCF_004514425.2_ASM451442v2_genomic.fna/checkm_result
[2024-01-24 12:38:08,766] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:08,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:08,786] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:08,786] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:08,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004514425.2_ASM451442v2_genomic.fna/markers.fasta)
[2024-01-24 12:38:08,787] [INFO] Task started: Blastn
[2024-01-24 12:38:08,787] [INFO] Running command: blastn -query GCF_004514425.2_ASM451442v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc12a6f76-aafc-4d39-94aa-c81bf0f7e720/dqc_reference/reference_markers_gtdb.fasta -out GCF_004514425.2_ASM451442v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:10,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:10,359] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:10,359] [INFO] Target genome list was writen to GCF_004514425.2_ASM451442v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:10,378] [INFO] Task started: fastANI
[2024-01-24 12:38:10,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgad90837a-fc50-4a42-b07b-d3240fa7ee91/GCF_004514425.2_ASM451442v2_genomic.fna.gz --refList GCF_004514425.2_ASM451442v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004514425.2_ASM451442v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:25,170] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,181] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:25,181] [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_004514435.1	s__Shinella sp004514435	99.9744	1699	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	conclusive
GCA_002364745.1	s__Shinella sp002364745	91.6908	1364	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.33	99.33	0.84	0.84	2	-
GCF_009826855.1	s__Shinella zoogloeoides	86.4991	1008	1766	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	86.4036	1134	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	86.3241	1119	1766	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	86.0755	1053	1766	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	86.0158	1167	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_003432075.1	s__Shinella sp003432075	85.7146	1080	1766	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	85.3624	1170	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_009827055.1	s__Shinella kummerowiae	85.2701	1165	1766	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	85.1141	1155	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220975.1	s__Mycoplana subbaraonis	81.328	885	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,183] [INFO] GTDB search result was written to GCF_004514425.2_ASM451442v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:25,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:25,186] [INFO] DFAST_QC result json was written to GCF_004514425.2_ASM451442v2_genomic.fna/dqc_result.json
[2024-01-24 12:38:25,186] [INFO] DFAST_QC completed!
[2024-01-24 12:38:25,187] [INFO] Total running time: 0h1m35s