[2023-06-04 17:44:23,362] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:44:23,365] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:44:23,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference
[2023-06-04 17:44:25,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:44:25,861] [INFO] Task started: Prodigal
[2023-06-04 17:44:25,861] [INFO] Running command: gunzip -c /var/lib/cwl/stga2e6d6e7-18b3-4a11-963d-647c362a1be6/GCA_004962935.1_ASM496293v1_genomic.fna.gz | prodigal -d GCA_004962935.1_ASM496293v1_genomic.fna/cds.fna -a GCA_004962935.1_ASM496293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:44:37,359] [INFO] Task succeeded: Prodigal
[2023-06-04 17:44:37,359] [INFO] Task started: HMMsearch
[2023-06-04 17:44:37,359] [INFO] Running command: hmmsearch --tblout GCA_004962935.1_ASM496293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/reference_markers.hmm GCA_004962935.1_ASM496293v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:44:37,619] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:44:37,621] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga2e6d6e7-18b3-4a11-963d-647c362a1be6/GCA_004962935.1_ASM496293v1_genomic.fna.gz]
[2023-06-04 17:44:37,670] [INFO] Query marker FASTA was written to GCA_004962935.1_ASM496293v1_genomic.fna/markers.fasta
[2023-06-04 17:44:37,671] [INFO] Task started: Blastn
[2023-06-04 17:44:37,671] [INFO] Running command: blastn -query GCA_004962935.1_ASM496293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/reference_markers.fasta -out GCA_004962935.1_ASM496293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:44:38,525] [INFO] Task succeeded: Blastn
[2023-06-04 17:44:38,530] [INFO] Selected 18 target genomes.
[2023-06-04 17:44:38,531] [INFO] Target genome list was writen to GCA_004962935.1_ASM496293v1_genomic.fna/target_genomes.txt
[2023-06-04 17:44:38,537] [INFO] Task started: fastANI
[2023-06-04 17:44:38,537] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e6d6e7-18b3-4a11-963d-647c362a1be6/GCA_004962935.1_ASM496293v1_genomic.fna.gz --refList GCA_004962935.1_ASM496293v1_genomic.fna/target_genomes.txt --output GCA_004962935.1_ASM496293v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:44:57,117] [INFO] Task succeeded: fastANI
[2023-06-04 17:44:57,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:44:57,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:44:57,131] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:44:57,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:44:57,131] [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	88.372	434	708	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	87.9339	441	708	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	86.3571	390	708	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.1663	396	708	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	85.8222	386	708	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	84.5427	401	708	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.2599	345	708	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	84.2448	378	708	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.0663	311	708	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	84.0318	384	708	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	83.8912	339	708	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	83.871	355	708	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	83.6224	372	708	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	83.2192	363	708	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.2095	371	708	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.7036	199	708	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.1523	195	708	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.1281	196	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:44:57,133] [INFO] DFAST Taxonomy check result was written to GCA_004962935.1_ASM496293v1_genomic.fna/tc_result.tsv
[2023-06-04 17:44:57,134] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:44:57,134] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:44:57,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/checkm_data
[2023-06-04 17:44:57,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:44:57,188] [INFO] Task started: CheckM
[2023-06-04 17:44:57,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004962935.1_ASM496293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004962935.1_ASM496293v1_genomic.fna/checkm_input GCA_004962935.1_ASM496293v1_genomic.fna/checkm_result
[2023-06-04 17:45:34,159] [INFO] Task succeeded: CheckM
[2023-06-04 17:45:34,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:45:34,186] [INFO] ===== Completeness check finished =====
[2023-06-04 17:45:34,186] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:45:34,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004962935.1_ASM496293v1_genomic.fna/markers.fasta)
[2023-06-04 17:45:34,187] [INFO] Task started: Blastn
[2023-06-04 17:45:34,187] [INFO] Running command: blastn -query GCA_004962935.1_ASM496293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96301ff6-8995-4e0b-8d50-6510677218fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_004962935.1_ASM496293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:45:35,698] [INFO] Task succeeded: Blastn
[2023-06-04 17:45:35,704] [INFO] Selected 15 target genomes.
[2023-06-04 17:45:35,704] [INFO] Target genome list was writen to GCA_004962935.1_ASM496293v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:45:35,806] [INFO] Task started: fastANI
[2023-06-04 17:45:35,806] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e6d6e7-18b3-4a11-963d-647c362a1be6/GCA_004962935.1_ASM496293v1_genomic.fna.gz --refList GCA_004962935.1_ASM496293v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004962935.1_ASM496293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:45:52,125] [INFO] Task succeeded: fastANI
[2023-06-04 17:45:52,152] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:45:52,153] [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_002294985.1	s__Mesorhizobium sp002294985	95.2446	483	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	conclusive
GCF_002294995.1	s__Mesorhizobium sp002294995	92.5465	474	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	90.0841	451	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_003952385.1	s__Mesorhizobium sp003952385	89.8711	459	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCA_004020545.1	s__Mesorhizobium sp004020545	89.6959	441	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_004791585.1	s__Mesorhizobium sp004791585	89.2547	446	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952465.1	s__Mesorhizobium sp003952465	89.1609	471	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_014843825.1	s__Mesorhizobium silamurunense	88.3657	435	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_003863365.1	s__Mesorhizobium tamadayense	87.9129	442	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016445.2	s__Mesorhizobium sp004016445	87.8106	450	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCA_001510895.1	s__Mesorhizobium loti_A	87.7647	422	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	87.464	410	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442815.1	s__Mesorhizobium sp006442815	86.7364	353	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003289945.1	s__Mesorhizobium hawassense	86.1663	396	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427725.1	s__Mesorhizobium sp000427725	85.901	388	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:45:52,156] [INFO] GTDB search result was written to GCA_004962935.1_ASM496293v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:45:52,156] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:45:52,161] [INFO] DFAST_QC result json was written to GCA_004962935.1_ASM496293v1_genomic.fna/dqc_result.json
[2023-06-04 17:45:52,161] [INFO] DFAST_QC completed!
[2023-06-04 17:45:52,161] [INFO] Total running time: 0h1m29s