[2024-01-24 13:17:58,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:58,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:58,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference
[2024-01-24 13:18:00,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,343] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,343] [INFO] Running command: gunzip -c /var/lib/cwl/stgd08baa7d-b3c6-4bf6-b49a-93b8fd27a2d5/GCF_000577275.2_LPU83_genomic.fna.gz | prodigal -d GCF_000577275.2_LPU83_genomic.fna/cds.fna -a GCF_000577275.2_LPU83_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:23,156] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:23,157] [INFO] Task started: HMMsearch
[2024-01-24 13:18:23,157] [INFO] Running command: hmmsearch --tblout GCF_000577275.2_LPU83_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/reference_markers.hmm GCF_000577275.2_LPU83_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:23,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:23,507] [INFO] Found 6/6 markers.
[2024-01-24 13:18:23,570] [INFO] Query marker FASTA was written to GCF_000577275.2_LPU83_genomic.fna/markers.fasta
[2024-01-24 13:18:23,571] [INFO] Task started: Blastn
[2024-01-24 13:18:23,571] [INFO] Running command: blastn -query GCF_000577275.2_LPU83_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/reference_markers.fasta -out GCF_000577275.2_LPU83_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:24,604] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:24,609] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:24,610] [INFO] Target genome list was writen to GCF_000577275.2_LPU83_genomic.fna/target_genomes.txt
[2024-01-24 13:18:24,615] [INFO] Task started: fastANI
[2024-01-24 13:18:24,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08baa7d-b3c6-4bf6-b49a-93b8fd27a2d5/GCF_000577275.2_LPU83_genomic.fna.gz --refList GCF_000577275.2_LPU83_genomic.fna/target_genomes.txt --output GCF_000577275.2_LPU83_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:42,116] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:42,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:42,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:42,129] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:18:42,129] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:42,130] [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 favelukesii	strain=LPU83	GCA_000577275.2	348824	348824	type	True	100.0	2492	2493	95	inconclusive
Rhizobium tibeticum		GCA_900108425.1	501024	501024	type	True	95.5879	1859	2493	95	inconclusive
Rhizobium tibeticum	strain=CGMCC 1.7071	GCA_900110205.1	501024	501024	type	True	95.5096	1884	2493	95	inconclusive
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	86.3095	1469	2493	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	85.5181	1441	2493	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.1593	1027	2493	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.0399	1075	2493	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	81.0035	1081	2493	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.9952	1072	2493	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5137	616	2493	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.0419	639	2493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,132] [INFO] DFAST Taxonomy check result was written to GCF_000577275.2_LPU83_genomic.fna/tc_result.tsv
[2024-01-24 13:18:42,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:42,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:42,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/checkm_data
[2024-01-24 13:18:42,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:42,210] [INFO] Task started: CheckM
[2024-01-24 13:18:42,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000577275.2_LPU83_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000577275.2_LPU83_genomic.fna/checkm_input GCF_000577275.2_LPU83_genomic.fna/checkm_result
[2024-01-24 13:19:47,611] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:47,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:47,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:47,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000577275.2_LPU83_genomic.fna/markers.fasta)
[2024-01-24 13:19:47,642] [INFO] Task started: Blastn
[2024-01-24 13:19:47,642] [INFO] Running command: blastn -query GCF_000577275.2_LPU83_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2443869-c248-4667-a097-e237a7ba4578/dqc_reference/reference_markers_gtdb.fasta -out GCF_000577275.2_LPU83_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:49,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:49,628] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:49,628] [INFO] Target genome list was writen to GCF_000577275.2_LPU83_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:49,640] [INFO] Task started: fastANI
[2024-01-24 13:19:49,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08baa7d-b3c6-4bf6-b49a-93b8fd27a2d5/GCF_000577275.2_LPU83_genomic.fna.gz --refList GCF_000577275.2_LPU83_genomic.fna/target_genomes_gtdb.txt --output GCF_000577275.2_LPU83_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:07,650] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:07,666] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:07,667] [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_000577275.2	s__Rhizobium favelukesii	100.0	2491	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.5244	99.59	99.23	0.94	0.89	3	conclusive
GCF_900110205.1	s__Rhizobium tibeticum	95.5113	1884	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.5244	99.98	99.98	0.99	0.99	2	-
GCF_000799845.1	s__Rhizobium sp000799845	95.0633	1779	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.2724	99.41	99.41	0.91	0.91	2	-
GCF_000282035.1	s__Rhizobium sp000282035	88.8209	1507	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.50	0.88	0.87	4	-
GCF_002211365.1	s__Rhizobium sp002211365	86.7485	1413	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.54	97.07	0.93	0.86	3	-
GCF_001542405.1	s__Rhizobium altiplani	86.3029	1468	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.38	95.34	0.86	0.71	19	-
GCA_900466605.1	s__Rhizobium sp900466605	86.0934	1358	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194695.1	s__Rhizobium sp014194695	85.5691	1364	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.49	98.48	0.95	0.94	4	-
GCF_000298315.2	s__Rhizobium grahamii	85.5375	1439	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.32	97.32	0.91	0.91	2	-
GCF_000746265.1	s__Rhizobium sp000746265	85.1058	1351	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746385.1	s__Rhizobium sp000746385	82.2305	1064	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.83	96.83	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:07,669] [INFO] GTDB search result was written to GCF_000577275.2_LPU83_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:07,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:07,674] [INFO] DFAST_QC result json was written to GCF_000577275.2_LPU83_genomic.fna/dqc_result.json
[2024-01-24 13:20:07,675] [INFO] DFAST_QC completed!
[2024-01-24 13:20:07,675] [INFO] Total running time: 0h2m9s