[2024-01-24 10:47:24,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,688] [INFO] DQC Reference Directory: /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference
[2024-01-24 10:47:26,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,626] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,626] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf43f83-4b78-4dcd-a041-c39fe4e22fe4/GCF_004137355.1_ASM413735v1_genomic.fna.gz | prodigal -d GCF_004137355.1_ASM413735v1_genomic.fna/cds.fna -a GCF_004137355.1_ASM413735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:41,040] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:41,040] [INFO] Task started: HMMsearch
[2024-01-24 10:47:41,040] [INFO] Running command: hmmsearch --tblout GCF_004137355.1_ASM413735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/reference_markers.hmm GCF_004137355.1_ASM413735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:41,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:41,360] [INFO] Found 6/6 markers.
[2024-01-24 10:47:41,402] [INFO] Query marker FASTA was written to GCF_004137355.1_ASM413735v1_genomic.fna/markers.fasta
[2024-01-24 10:47:41,403] [INFO] Task started: Blastn
[2024-01-24 10:47:41,403] [INFO] Running command: blastn -query GCF_004137355.1_ASM413735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/reference_markers.fasta -out GCF_004137355.1_ASM413735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:42,475] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:42,478] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:42,479] [INFO] Target genome list was writen to GCF_004137355.1_ASM413735v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,485] [INFO] Task started: fastANI
[2024-01-24 10:47:42,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf43f83-4b78-4dcd-a041-c39fe4e22fe4/GCF_004137355.1_ASM413735v1_genomic.fna.gz --refList GCF_004137355.1_ASM413735v1_genomic.fna/target_genomes.txt --output GCF_004137355.1_ASM413735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:57,161] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:57,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:57,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:57,172] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:57,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:57,173] [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
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	100.0	1643	1645	95	conclusive
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	90.9576	1415	1645	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	90.8971	1261	1645	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	81.724	916	1645	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	80.4536	693	1645	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	80.4011	728	1645	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	80.3491	735	1645	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2634	725	1645	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.2233	758	1645	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.1431	660	1645	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.7923	621	1645	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.6189	642	1645	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	79.4505	682	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,175] [INFO] DFAST Taxonomy check result was written to GCF_004137355.1_ASM413735v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:57,176] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:57,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:57,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/checkm_data
[2024-01-24 10:47:57,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:57,231] [INFO] Task started: CheckM
[2024-01-24 10:47:57,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137355.1_ASM413735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137355.1_ASM413735v1_genomic.fna/checkm_input GCF_004137355.1_ASM413735v1_genomic.fna/checkm_result
[2024-01-24 10:48:40,743] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:40,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:40,771] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:40,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:40,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137355.1_ASM413735v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:40,773] [INFO] Task started: Blastn
[2024-01-24 10:48:40,773] [INFO] Running command: blastn -query GCF_004137355.1_ASM413735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6769dc78-e108-4fe6-a63e-ad6ef85f39a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137355.1_ASM413735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:42,920] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:42,924] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:42,924] [INFO] Target genome list was writen to GCF_004137355.1_ASM413735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:42,932] [INFO] Task started: fastANI
[2024-01-24 10:48:42,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf43f83-4b78-4dcd-a041-c39fe4e22fe4/GCF_004137355.1_ASM413735v1_genomic.fna.gz --refList GCF_004137355.1_ASM413735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137355.1_ASM413735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:55,824] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:55,838] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:55,839] [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
GCA_900465605.1	s__Allorhizobium sp900465605	95.707	1421	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.96	95.85	0.92	0.91	5	conclusive
GCA_900466005.1	s__Allorhizobium sp900466005	91.695	1445	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_014126615.1	s__Allorhizobium thiooxidans	90.9625	1414	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337715.1	s__Allorhizobium lividum	90.8971	1261	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518785.1	s__Allorhizobium selenitireducens	81.7367	916	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	81.2976	864	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473245.1	s__Allorhizobium sp900473245	80.6303	795	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.81	98.34	0.95	0.93	20	-
GCF_002600635.1	s__Allorhizobium sp002600635	80.5313	845	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	80.4548	693	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305935.1	s__Rhizobium sp017305935	79.5964	660	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429285.1	s__Ensifer sp001429285	79.3473	674	1645	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.69	95.18	0.90	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:55,841] [INFO] GTDB search result was written to GCF_004137355.1_ASM413735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:55,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:55,845] [INFO] DFAST_QC result json was written to GCF_004137355.1_ASM413735v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:55,845] [INFO] DFAST_QC completed!
[2024-01-24 10:48:55,845] [INFO] Total running time: 0h1m31s