[2024-01-25 19:10:20,874] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:20,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:20,876] [INFO] DQC Reference Directory: /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference
[2024-01-25 19:10:22,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:22,081] [INFO] Task started: Prodigal
[2024-01-25 19:10:22,081] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4430976-3fb1-46fc-a08c-c8eb36c32db5/GCF_000419765.1_ASM41976v1_genomic.fna.gz | prodigal -d GCF_000419765.1_ASM41976v1_genomic.fna/cds.fna -a GCF_000419765.1_ASM41976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:40,624] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:40,625] [INFO] Task started: HMMsearch
[2024-01-25 19:10:40,625] [INFO] Running command: hmmsearch --tblout GCF_000419765.1_ASM41976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/reference_markers.hmm GCF_000419765.1_ASM41976v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:41,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:41,049] [INFO] Found 6/6 markers.
[2024-01-25 19:10:41,103] [INFO] Query marker FASTA was written to GCF_000419765.1_ASM41976v1_genomic.fna/markers.fasta
[2024-01-25 19:10:41,103] [INFO] Task started: Blastn
[2024-01-25 19:10:41,103] [INFO] Running command: blastn -query GCF_000419765.1_ASM41976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/reference_markers.fasta -out GCF_000419765.1_ASM41976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:42,056] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:42,059] [INFO] Selected 14 target genomes.
[2024-01-25 19:10:42,059] [INFO] Target genome list was writen to GCF_000419765.1_ASM41976v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:42,065] [INFO] Task started: fastANI
[2024-01-25 19:10:42,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4430976-3fb1-46fc-a08c-c8eb36c32db5/GCF_000419765.1_ASM41976v1_genomic.fna.gz --refList GCF_000419765.1_ASM41976v1_genomic.fna/target_genomes.txt --output GCF_000419765.1_ASM41976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:02,149] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:02,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:02,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:02,159] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:11:02,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:02,159] [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 mongolense	strain=USDA 1844	GCA_000419765.1	57676	57676	type	True	100.0	2338	2341	95	conclusive
Rhizobium mongolense	strain=USDA 1844	GCA_007827505.1	57676	57676	type	True	99.9971	2337	2341	95	conclusive
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	96.0069	1821	2341	95	conclusive
Rhizobium gallicum	strain=R602	GCA_000816845.1	56730	56730	type	True	94.3684	1793	2341	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	81.8918	1213	2341	95	below_threshold
Rhizobium vallis	strain=CCBAU 65647	GCA_003985155.1	634290	634290	type	True	81.7137	1117	2341	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	81.674	1159	2341	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	81.6024	1146	2341	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	81.5381	1156	2341	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	81.3193	1096	2341	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	81.309	1145	2341	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	81.2397	1119	2341	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.4294	637	2341	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.1777	645	2341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:02,161] [INFO] DFAST Taxonomy check result was written to GCF_000419765.1_ASM41976v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:02,161] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:02,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:02,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/checkm_data
[2024-01-25 19:11:02,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:02,229] [INFO] Task started: CheckM
[2024-01-25 19:11:02,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000419765.1_ASM41976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000419765.1_ASM41976v1_genomic.fna/checkm_input GCF_000419765.1_ASM41976v1_genomic.fna/checkm_result
[2024-01-25 19:11:54,978] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:54,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:54,997] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:54,997] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:54,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000419765.1_ASM41976v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:54,998] [INFO] Task started: Blastn
[2024-01-25 19:11:54,998] [INFO] Running command: blastn -query GCF_000419765.1_ASM41976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba042048-f075-4ab4-9795-6c9405525440/dqc_reference/reference_markers_gtdb.fasta -out GCF_000419765.1_ASM41976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:56,951] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:56,954] [INFO] Selected 6 target genomes.
[2024-01-25 19:11:56,955] [INFO] Target genome list was writen to GCF_000419765.1_ASM41976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:56,960] [INFO] Task started: fastANI
[2024-01-25 19:11:56,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4430976-3fb1-46fc-a08c-c8eb36c32db5/GCF_000419765.1_ASM41976v1_genomic.fna.gz --refList GCF_000419765.1_ASM41976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000419765.1_ASM41976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:08,341] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:08,346] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:08,346] [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_000419765.1	s__Rhizobium mongolense	100.0	2338	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	96.0481	99.21	97.63	0.93	0.80	4	conclusive
GCF_900099775.1	s__Rhizobium loessense	96.0069	1821	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	96.0481	N/A	N/A	N/A	N/A	1	-
GCF_015353075.1	s__Rhizobium yanglingense	95.602	1902	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.6157	97.95	97.94	0.79	0.78	3	-
GCF_000816845.1	s__Rhizobium gallicum	94.3538	1794	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.4207	99.69	99.44	0.97	0.94	3	-
GCF_001908375.1	s__Rhizobium etli_B	92.1097	1701	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.26	99.00	0.92	0.87	3	-
GCF_900169785.1	s__Rhizobium sullae	88.8047	1627	2341	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.06	97.50	0.88	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:08,348] [INFO] GTDB search result was written to GCF_000419765.1_ASM41976v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:08,348] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:08,351] [INFO] DFAST_QC result json was written to GCF_000419765.1_ASM41976v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:08,351] [INFO] DFAST_QC completed!
[2024-01-25 19:12:08,351] [INFO] Total running time: 0h1m47s