[2024-01-24 15:19:50,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:50,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:50,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference
[2024-01-24 15:19:51,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:51,463] [INFO] Task started: Prodigal
[2024-01-24 15:19:51,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c11c716-b926-4b53-b0ea-686e15bb007f/GCF_002968635.1_ASM296863v1_genomic.fna.gz | prodigal -d GCF_002968635.1_ASM296863v1_genomic.fna/cds.fna -a GCF_002968635.1_ASM296863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:08,542] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:08,542] [INFO] Task started: HMMsearch
[2024-01-24 15:20:08,542] [INFO] Running command: hmmsearch --tblout GCF_002968635.1_ASM296863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/reference_markers.hmm GCF_002968635.1_ASM296863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:08,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:08,880] [INFO] Found 6/6 markers.
[2024-01-24 15:20:08,928] [INFO] Query marker FASTA was written to GCF_002968635.1_ASM296863v1_genomic.fna/markers.fasta
[2024-01-24 15:20:08,929] [INFO] Task started: Blastn
[2024-01-24 15:20:08,929] [INFO] Running command: blastn -query GCF_002968635.1_ASM296863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/reference_markers.fasta -out GCF_002968635.1_ASM296863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:09,898] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:09,910] [INFO] Selected 12 target genomes.
[2024-01-24 15:20:09,911] [INFO] Target genome list was writen to GCF_002968635.1_ASM296863v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:09,919] [INFO] Task started: fastANI
[2024-01-24 15:20:09,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c11c716-b926-4b53-b0ea-686e15bb007f/GCF_002968635.1_ASM296863v1_genomic.fna.gz --refList GCF_002968635.1_ASM296863v1_genomic.fna/target_genomes.txt --output GCF_002968635.1_ASM296863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:26,267] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:26,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:26,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:26,283] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:26,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:26,284] [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
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	100.0	1934	1935	95	conclusive
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	88.9095	1404	1935	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	82.6382	1188	1935	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	82.5836	1175	1935	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	82.1484	1124	1935	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	81.6718	1112	1935	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.7793	594	1935	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	79.5498	729	1935	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.5261	738	1935	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.4758	698	1935	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.1967	625	1935	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.9887	679	1935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:26,285] [INFO] DFAST Taxonomy check result was written to GCF_002968635.1_ASM296863v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:26,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:26,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:26,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/checkm_data
[2024-01-24 15:20:26,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:26,348] [INFO] Task started: CheckM
[2024-01-24 15:20:26,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002968635.1_ASM296863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002968635.1_ASM296863v1_genomic.fna/checkm_input GCF_002968635.1_ASM296863v1_genomic.fna/checkm_result
[2024-01-24 15:21:16,503] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:16,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:16,529] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:16,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:16,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002968635.1_ASM296863v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:16,530] [INFO] Task started: Blastn
[2024-01-24 15:21:16,530] [INFO] Running command: blastn -query GCF_002968635.1_ASM296863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84f25048-8394-4624-92dd-ba96a0079ba8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002968635.1_ASM296863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:18,445] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:18,451] [INFO] Selected 12 target genomes.
[2024-01-24 15:21:18,451] [INFO] Target genome list was writen to GCF_002968635.1_ASM296863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:18,461] [INFO] Task started: fastANI
[2024-01-24 15:21:18,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c11c716-b926-4b53-b0ea-686e15bb007f/GCF_002968635.1_ASM296863v1_genomic.fna.gz --refList GCF_002968635.1_ASM296863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002968635.1_ASM296863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:34,751] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:34,817] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:34,818] [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_002968635.1	s__Neorhizobium alkalisoli	100.0	1934	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900469955.1	s__Neorhizobium sp900469955	93.7265	1549	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	88.8971	1406	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCF_900177415.1	s__Neorhizobium oryzae_A	83.2373	1149	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985895.1	s__Neorhizobium galegae_B	83.0249	1169	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.06	98.00	0.96	0.95	4	-
GCF_000282095.2	s__Neorhizobium sp000282095	82.8028	1176	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	82.7427	1169	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002968845.1	s__Neorhizobium tomejilense	82.7093	1196	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.02	95.22	0.90	0.84	9	-
GCA_000985875.1	s__Neorhizobium galegae_C	82.7057	1192	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_003425685.1	s__Neorhizobium sp003425685	82.4405	1187	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005825.1	s__Neorhizobium sp001005825	80.9922	922	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004358025.1	s__Neorhizobium deserti	80.1625	813	1935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:34,820] [INFO] GTDB search result was written to GCF_002968635.1_ASM296863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:34,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:34,824] [INFO] DFAST_QC result json was written to GCF_002968635.1_ASM296863v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:34,824] [INFO] DFAST_QC completed!
[2024-01-24 15:21:34,824] [INFO] Total running time: 0h1m45s