[2024-01-24 13:18:32,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference
[2024-01-24 13:18:34,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,417] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg1761eed7-0452-4a47-976f-7e7a18904cf6/GCF_000427465.1_ASM42746v1_genomic.fna.gz | prodigal -d GCF_000427465.1_ASM42746v1_genomic.fna/cds.fna -a GCF_000427465.1_ASM42746v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:55,768] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:55,768] [INFO] Task started: HMMsearch
[2024-01-24 13:18:55,768] [INFO] Running command: hmmsearch --tblout GCF_000427465.1_ASM42746v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/reference_markers.hmm GCF_000427465.1_ASM42746v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:56,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:56,149] [INFO] Found 6/6 markers.
[2024-01-24 13:18:56,217] [INFO] Query marker FASTA was written to GCF_000427465.1_ASM42746v1_genomic.fna/markers.fasta
[2024-01-24 13:18:56,217] [INFO] Task started: Blastn
[2024-01-24 13:18:56,217] [INFO] Running command: blastn -query GCF_000427465.1_ASM42746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/reference_markers.fasta -out GCF_000427465.1_ASM42746v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:57,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:57,340] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:57,340] [INFO] Target genome list was writen to GCF_000427465.1_ASM42746v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:57,344] [INFO] Task started: fastANI
[2024-01-24 13:18:57,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg1761eed7-0452-4a47-976f-7e7a18904cf6/GCF_000427465.1_ASM42746v1_genomic.fna.gz --refList GCF_000427465.1_ASM42746v1_genomic.fna/target_genomes.txt --output GCF_000427465.1_ASM42746v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:12,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:12,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:12,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:12,529] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:12,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:12,529] [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 arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	100.0	2279	2280	95	conclusive
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	90.4827	1532	2280	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	90.4115	1605	2280	95	below_threshold
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	90.4033	1669	2280	95	below_threshold
Sinorhizobium medicae	strain=A321	GCA_009599935.1	110321	110321	type	True	86.1046	1565	2280	95	below_threshold
Sinorhizobium medicae	strain=USDA1037	GCA_007827695.1	110321	110321	type	True	86.0747	1524	2280	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.1545	747	2280	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.4111	750	2280	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	79.3022	620	2280	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.982	605	2280	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.3606	529	2280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,533] [INFO] DFAST Taxonomy check result was written to GCF_000427465.1_ASM42746v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:12,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:12,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:12,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/checkm_data
[2024-01-24 13:19:12,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:12,608] [INFO] Task started: CheckM
[2024-01-24 13:19:12,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000427465.1_ASM42746v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000427465.1_ASM42746v1_genomic.fna/checkm_input GCF_000427465.1_ASM42746v1_genomic.fna/checkm_result
[2024-01-24 13:20:09,375] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:09,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:09,409] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:09,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:09,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000427465.1_ASM42746v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:09,410] [INFO] Task started: Blastn
[2024-01-24 13:20:09,410] [INFO] Running command: blastn -query GCF_000427465.1_ASM42746v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ff43b5e-b64c-494b-b8a8-730723336ee0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000427465.1_ASM42746v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:11,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:11,529] [INFO] Selected 6 target genomes.
[2024-01-24 13:20:11,530] [INFO] Target genome list was writen to GCF_000427465.1_ASM42746v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:11,538] [INFO] Task started: fastANI
[2024-01-24 13:20:11,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg1761eed7-0452-4a47-976f-7e7a18904cf6/GCF_000427465.1_ASM42746v1_genomic.fna.gz --refList GCF_000427465.1_ASM42746v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000427465.1_ASM42746v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:21,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:21,921] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:21,922] [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_000427465.1	s__Sinorhizobium arboris	100.0	2279	2280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876815.1	s__Sinorhizobium meliloti	90.4065	1668	2280	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	90.0887	1671	2280	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	89.8171	1612	2280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	97.48	0.86	0.81	5	-
GCF_007827695.1	s__Sinorhizobium medicae	86.067	1525	2280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.40	99.02	0.92	0.89	63	-
GCF_001651875.1	s__Sinorhizobium saheli	83.9694	1264	2280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:21,925] [INFO] GTDB search result was written to GCF_000427465.1_ASM42746v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:21,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:21,928] [INFO] DFAST_QC result json was written to GCF_000427465.1_ASM42746v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:21,928] [INFO] DFAST_QC completed!
[2024-01-24 13:20:21,928] [INFO] Total running time: 0h1m49s