[2024-01-24 13:22:00,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference
[2024-01-24 13:22:02,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:02,140] [INFO] Task started: Prodigal
[2024-01-24 13:22:02,141] [INFO] Running command: gunzip -c /var/lib/cwl/stga28de41f-b815-4522-8324-db326021479d/GCF_017876815.1_ASM1787681v1_genomic.fna.gz | prodigal -d GCF_017876815.1_ASM1787681v1_genomic.fna/cds.fna -a GCF_017876815.1_ASM1787681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:32,624] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:32,624] [INFO] Task started: HMMsearch
[2024-01-24 13:22:32,624] [INFO] Running command: hmmsearch --tblout GCF_017876815.1_ASM1787681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/reference_markers.hmm GCF_017876815.1_ASM1787681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:32,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:32,997] [INFO] Found 6/6 markers.
[2024-01-24 13:22:33,056] [INFO] Query marker FASTA was written to GCF_017876815.1_ASM1787681v1_genomic.fna/markers.fasta
[2024-01-24 13:22:33,056] [INFO] Task started: Blastn
[2024-01-24 13:22:33,056] [INFO] Running command: blastn -query GCF_017876815.1_ASM1787681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/reference_markers.fasta -out GCF_017876815.1_ASM1787681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:34,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:34,184] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:34,184] [INFO] Target genome list was writen to GCF_017876815.1_ASM1787681v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:34,186] [INFO] Task started: fastANI
[2024-01-24 13:22:34,186] [INFO] Running command: fastANI --query /var/lib/cwl/stga28de41f-b815-4522-8324-db326021479d/GCF_017876815.1_ASM1787681v1_genomic.fna.gz --refList GCF_017876815.1_ASM1787681v1_genomic.fna/target_genomes.txt --output GCF_017876815.1_ASM1787681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:51,913] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:51,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:51,923] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:51,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:51,923] [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 meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	100.0	2438	2446	95	conclusive
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	99.8838	2071	2446	95	conclusive
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	99.8756	2225	2446	95	conclusive
Sinorhizobium arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	90.3973	1663	2446	95	below_threshold
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	87.4233	1728	2446	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.6319	769	2446	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.3025	917	2446	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.1591	771	2446	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.8586	746	2446	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.1734	613	2446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,925] [INFO] DFAST Taxonomy check result was written to GCF_017876815.1_ASM1787681v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:51,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:51,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:51,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/checkm_data
[2024-01-24 13:22:51,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:51,997] [INFO] Task started: CheckM
[2024-01-24 13:22:51,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876815.1_ASM1787681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876815.1_ASM1787681v1_genomic.fna/checkm_input GCF_017876815.1_ASM1787681v1_genomic.fna/checkm_result
[2024-01-24 13:24:10,182] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:10,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:10,208] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:10,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:10,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876815.1_ASM1787681v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:10,209] [INFO] Task started: Blastn
[2024-01-24 13:24:10,209] [INFO] Running command: blastn -query GCF_017876815.1_ASM1787681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cdad0b1-be9a-48f0-9cae-ed0cc492f345/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876815.1_ASM1787681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:12,287] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:12,291] [INFO] Selected 5 target genomes.
[2024-01-24 13:24:12,291] [INFO] Target genome list was writen to GCF_017876815.1_ASM1787681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:12,297] [INFO] Task started: fastANI
[2024-01-24 13:24:12,297] [INFO] Running command: fastANI --query /var/lib/cwl/stga28de41f-b815-4522-8324-db326021479d/GCF_017876815.1_ASM1787681v1_genomic.fna.gz --refList GCF_017876815.1_ASM1787681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876815.1_ASM1787681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:23,208] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:23,219] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:23,219] [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_017876815.1	s__Sinorhizobium meliloti	100.0	2436	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.94	97.48	0.91	0.82	239	conclusive
GCA_000421085.1	s__Sinorhizobium sp000421085	94.3211	1741	2446	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	93.843	1742	2446	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	90.3831	1665	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827695.1	s__Sinorhizobium medicae	87.3652	1715	2446	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.40	99.02	0.92	0.89	63	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:23,221] [INFO] GTDB search result was written to GCF_017876815.1_ASM1787681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:23,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:23,224] [INFO] DFAST_QC result json was written to GCF_017876815.1_ASM1787681v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:23,224] [INFO] DFAST_QC completed!
[2024-01-24 13:24:23,224] [INFO] Total running time: 0h2m22s