[2024-01-25 19:35:50,982] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:50,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:50,985] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference
[2024-01-25 19:35:52,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,169] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,169] [INFO] Running command: gunzip -c /var/lib/cwl/stg348d77c7-2b7f-4146-9478-59389ce56ee3/GCF_009599935.1_ASM959993v1_genomic.fna.gz | prodigal -d GCF_009599935.1_ASM959993v1_genomic.fna/cds.fna -a GCF_009599935.1_ASM959993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:10,206] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:10,206] [INFO] Task started: HMMsearch
[2024-01-25 19:36:10,206] [INFO] Running command: hmmsearch --tblout GCF_009599935.1_ASM959993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/reference_markers.hmm GCF_009599935.1_ASM959993v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:10,627] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:10,628] [INFO] Found 6/6 markers.
[2024-01-25 19:36:10,681] [INFO] Query marker FASTA was written to GCF_009599935.1_ASM959993v1_genomic.fna/markers.fasta
[2024-01-25 19:36:10,681] [INFO] Task started: Blastn
[2024-01-25 19:36:10,681] [INFO] Running command: blastn -query GCF_009599935.1_ASM959993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/reference_markers.fasta -out GCF_009599935.1_ASM959993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:11,500] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:11,503] [INFO] Selected 11 target genomes.
[2024-01-25 19:36:11,503] [INFO] Target genome list was writen to GCF_009599935.1_ASM959993v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:11,506] [INFO] Task started: fastANI
[2024-01-25 19:36:11,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg348d77c7-2b7f-4146-9478-59389ce56ee3/GCF_009599935.1_ASM959993v1_genomic.fna.gz --refList GCF_009599935.1_ASM959993v1_genomic.fna/target_genomes.txt --output GCF_009599935.1_ASM959993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:26,775] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:26,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:26,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:26,783] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:36:26,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:26,784] [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
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	100.0	2249	2274	95	conclusive
Sinorhizobium medicae	strain=USDA1037	GCA_007827695.1	110321	110321	type	True	99.9394	2117	2274	95	conclusive
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	87.4125	1731	2274	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	87.38	1554	2274	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	87.3693	1675	2274	95	below_threshold
Sinorhizobium arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	86.0378	1580	2274	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.6432	643	2274	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.643	707	2274	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.6091	820	2274	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.0784	643	2274	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	78.7932	545	2274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:26,785] [INFO] DFAST Taxonomy check result was written to GCF_009599935.1_ASM959993v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:26,785] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:26,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:26,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/checkm_data
[2024-01-25 19:36:26,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:26,855] [INFO] Task started: CheckM
[2024-01-25 19:36:26,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009599935.1_ASM959993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009599935.1_ASM959993v1_genomic.fna/checkm_input GCF_009599935.1_ASM959993v1_genomic.fna/checkm_result
[2024-01-25 19:37:16,492] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:16,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:16,515] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:16,515] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:16,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009599935.1_ASM959993v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:16,515] [INFO] Task started: Blastn
[2024-01-25 19:37:16,516] [INFO] Running command: blastn -query GCF_009599935.1_ASM959993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d78bca-37ee-4548-99a4-4beb75965f5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009599935.1_ASM959993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:18,067] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:18,070] [INFO] Selected 7 target genomes.
[2024-01-25 19:37:18,070] [INFO] Target genome list was writen to GCF_009599935.1_ASM959993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:18,074] [INFO] Task started: fastANI
[2024-01-25 19:37:18,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg348d77c7-2b7f-4146-9478-59389ce56ee3/GCF_009599935.1_ASM959993v1_genomic.fna.gz --refList GCF_009599935.1_ASM959993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009599935.1_ASM959993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:28,584] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:28,589] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:28,589] [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_007827695.1	s__Sinorhizobium medicae	99.9394	2117	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.40	99.02	0.92	0.89	63	conclusive
GCF_017876815.1	s__Sinorhizobium meliloti	87.3776	1736	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.94	97.48	0.91	0.82	239	-
GCA_000421085.1	s__Sinorhizobium sp000421085	86.7344	1643	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375585.1	s__Sinorhizobium meliloti_A	86.5729	1619	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	97.48	0.86	0.81	5	-
GCF_000427465.1	s__Sinorhizobium arboris	86.0281	1582	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442315.1	s__Mesorhizobium sp006442315	77.48	408	2274	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:28,591] [INFO] GTDB search result was written to GCF_009599935.1_ASM959993v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:28,591] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:28,594] [INFO] DFAST_QC result json was written to GCF_009599935.1_ASM959993v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:28,595] [INFO] DFAST_QC completed!
[2024-01-25 19:37:28,595] [INFO] Total running time: 0h1m38s