[2024-01-24 13:19:29,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:29,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:29,059] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference
[2024-01-24 13:19:30,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:30,435] [INFO] Task started: Prodigal
[2024-01-24 13:19:30,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg85cc4ce5-9455-4030-9d5b-081d9cbd5524/GCF_014843825.1_ASM1484382v1_genomic.fna.gz | prodigal -d GCF_014843825.1_ASM1484382v1_genomic.fna/cds.fna -a GCF_014843825.1_ASM1484382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:50,430] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:50,431] [INFO] Task started: HMMsearch
[2024-01-24 13:19:50,431] [INFO] Running command: hmmsearch --tblout GCF_014843825.1_ASM1484382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/reference_markers.hmm GCF_014843825.1_ASM1484382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:50,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:50,762] [INFO] Found 6/6 markers.
[2024-01-24 13:19:50,823] [INFO] Query marker FASTA was written to GCF_014843825.1_ASM1484382v1_genomic.fna/markers.fasta
[2024-01-24 13:19:50,823] [INFO] Task started: Blastn
[2024-01-24 13:19:50,823] [INFO] Running command: blastn -query GCF_014843825.1_ASM1484382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/reference_markers.fasta -out GCF_014843825.1_ASM1484382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:51,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:51,916] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:51,917] [INFO] Target genome list was writen to GCF_014843825.1_ASM1484382v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:51,926] [INFO] Task started: fastANI
[2024-01-24 13:19:51,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg85cc4ce5-9455-4030-9d5b-081d9cbd5524/GCF_014843825.1_ASM1484382v1_genomic.fna.gz --refList GCF_014843825.1_ASM1484382v1_genomic.fna/target_genomes.txt --output GCF_014843825.1_ASM1484382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:12,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:12,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:12,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:12,523] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:12,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:12,524] [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
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	100.0	2097	2118	95	conclusive
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	90.7301	1626	2118	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	87.391	1511	2118	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	87.3379	1458	2118	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.6524	1480	2118	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.0322	1222	2118	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	84.4074	1389	2118	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.3335	1215	2118	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	84.2551	1371	2118	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.1533	1325	2118	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.5765	661	2118	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.5639	664	2118	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.469	583	2118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:12,525] [INFO] DFAST Taxonomy check result was written to GCF_014843825.1_ASM1484382v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:12,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:12,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:12,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/checkm_data
[2024-01-24 13:20:12,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:12,594] [INFO] Task started: CheckM
[2024-01-24 13:20:12,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014843825.1_ASM1484382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014843825.1_ASM1484382v1_genomic.fna/checkm_input GCF_014843825.1_ASM1484382v1_genomic.fna/checkm_result
[2024-01-24 13:21:08,042] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:08,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:08,070] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:08,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:08,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014843825.1_ASM1484382v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:08,071] [INFO] Task started: Blastn
[2024-01-24 13:21:08,071] [INFO] Running command: blastn -query GCF_014843825.1_ASM1484382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb61dc25-fbcf-426f-a77e-6765c67909da/dqc_reference/reference_markers_gtdb.fasta -out GCF_014843825.1_ASM1484382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:10,291] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:10,305] [INFO] Selected 11 target genomes.
[2024-01-24 13:21:10,305] [INFO] Target genome list was writen to GCF_014843825.1_ASM1484382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:10,325] [INFO] Task started: fastANI
[2024-01-24 13:21:10,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg85cc4ce5-9455-4030-9d5b-081d9cbd5524/GCF_014843825.1_ASM1484382v1_genomic.fna.gz --refList GCF_014843825.1_ASM1484382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014843825.1_ASM1484382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:29,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:29,755] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:29,755] [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_014843825.1	s__Mesorhizobium silamurunense	100.0	2097	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	conclusive
GCF_003952385.1	s__Mesorhizobium sp003952385	91.3779	1604	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_003863365.1	s__Mesorhizobium tamadayense	90.7483	1622	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952465.1	s__Mesorhizobium sp003952465	90.185	1666	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCA_004963905.1	s__Mesorhizobium sp004963905	90.1391	1540	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	90.05	1586	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCA_004020545.1	s__Mesorhizobium sp004020545	89.9979	1557	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_003952485.1	s__Mesorhizobium sp003952485	89.8649	1604	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_002294995.1	s__Mesorhizobium sp002294995	89.8261	1495	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294985.1	s__Mesorhizobium sp002294985	89.6644	1464	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	-
GCA_000824825.2	s__Mesorhizobium sp000824825	89.3752	1523	2118	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:29,757] [INFO] GTDB search result was written to GCF_014843825.1_ASM1484382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:29,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:29,761] [INFO] DFAST_QC result json was written to GCF_014843825.1_ASM1484382v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:29,761] [INFO] DFAST_QC completed!
[2024-01-24 13:21:29,761] [INFO] Total running time: 0h2m1s