[2024-01-25 19:55:50,438] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:50,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:50,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference
[2024-01-25 19:55:51,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:51,622] [INFO] Task started: Prodigal
[2024-01-25 19:55:51,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e3f52c1-f133-414b-9d38-dbfde4487194/GCF_009649785.1_ASM964978v1_genomic.fna.gz | prodigal -d GCF_009649785.1_ASM964978v1_genomic.fna/cds.fna -a GCF_009649785.1_ASM964978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:07,125] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:07,125] [INFO] Task started: HMMsearch
[2024-01-25 19:56:07,125] [INFO] Running command: hmmsearch --tblout GCF_009649785.1_ASM964978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/reference_markers.hmm GCF_009649785.1_ASM964978v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:07,401] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:07,402] [INFO] Found 6/6 markers.
[2024-01-25 19:56:07,450] [INFO] Query marker FASTA was written to GCF_009649785.1_ASM964978v1_genomic.fna/markers.fasta
[2024-01-25 19:56:07,451] [INFO] Task started: Blastn
[2024-01-25 19:56:07,451] [INFO] Running command: blastn -query GCF_009649785.1_ASM964978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/reference_markers.fasta -out GCF_009649785.1_ASM964978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:08,352] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:08,355] [INFO] Selected 9 target genomes.
[2024-01-25 19:56:08,355] [INFO] Target genome list was writen to GCF_009649785.1_ASM964978v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:08,358] [INFO] Task started: fastANI
[2024-01-25 19:56:08,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3f52c1-f133-414b-9d38-dbfde4487194/GCF_009649785.1_ASM964978v1_genomic.fna.gz --refList GCF_009649785.1_ASM964978v1_genomic.fna/target_genomes.txt --output GCF_009649785.1_ASM964978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:19,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:19,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:19,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:19,297] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:56:19,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:56:19,297] [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
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	89.301	1363	1861	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	87.834	1416	1861	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	87.8036	1374	1861	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	87.8015	1425	1861	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_900045375.1	358	358	suspected-type	True	87.7508	1437	1861	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	87.0717	1307	1861	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.0711	558	1861	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.7115	630	1861	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4424	494	1861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:19,299] [INFO] DFAST Taxonomy check result was written to GCF_009649785.1_ASM964978v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:19,299] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:19,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:19,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/checkm_data
[2024-01-25 19:56:19,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:19,353] [INFO] Task started: CheckM
[2024-01-25 19:56:19,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649785.1_ASM964978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649785.1_ASM964978v1_genomic.fna/checkm_input GCF_009649785.1_ASM964978v1_genomic.fna/checkm_result
[2024-01-25 19:57:02,977] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:02,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:02,995] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:02,995] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:02,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649785.1_ASM964978v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:02,995] [INFO] Task started: Blastn
[2024-01-25 19:57:02,996] [INFO] Running command: blastn -query GCF_009649785.1_ASM964978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcac352a9-0213-4c18-bccd-3c1104da4f56/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649785.1_ASM964978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:04,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:04,869] [INFO] Selected 11 target genomes.
[2024-01-25 19:57:04,869] [INFO] Target genome list was writen to GCF_009649785.1_ASM964978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:04,889] [INFO] Task started: fastANI
[2024-01-25 19:57:04,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e3f52c1-f133-414b-9d38-dbfde4487194/GCF_009649785.1_ASM964978v1_genomic.fna.gz --refList GCF_009649785.1_ASM964978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649785.1_ASM964978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:19,617] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:19,625] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:19,625] [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_009649785.1	s__Agrobacterium fabacearum	100.0	1857	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.40	96.96	0.89	0.76	243	conclusive
GCA_000949895.1	s__Agrobacterium arsenijevicii	90.7949	1424	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949865.1	s__Agrobacterium nepotum	89.9847	1372	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669145.1	s__Agrobacterium oryzihabitans	89.3245	1360	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.96	97.17	0.87	0.79	9	-
GCF_001541315.1	s__Agrobacterium tumefaciens	87.8015	1425	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.87	95.73	0.89	0.83	248	-
GCF_013337285.1	s__Agrobacterium tumefaciens_H	87.5767	1391	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.07	97.88	0.96	0.94	4	-
GCF_002943835.1	s__Agrobacterium deltaense	87.5578	1394	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.62	95.20	0.87	0.77	64	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	87.5296	1368	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_000092025.1	s__Agrobacterium fabrum	87.2982	1450	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.52	95.41	0.93	0.85	28	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	87.258	1314	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005221325.1	s__Agrobacterium sp900012625	87.1984	1430	1861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	99.19	97.65	0.98	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:19,626] [INFO] GTDB search result was written to GCF_009649785.1_ASM964978v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:19,627] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:19,630] [INFO] DFAST_QC result json was written to GCF_009649785.1_ASM964978v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:19,630] [INFO] DFAST_QC completed!
[2024-01-25 19:57:19,630] [INFO] Total running time: 0h1m29s