[2024-01-25 20:19:20,723] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference
[2024-01-25 20:19:21,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,868] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b5f9942-38f7-43d3-93da-d1addb2cb1f1/GCF_002284575.1_ASM228457v1_genomic.fna.gz | prodigal -d GCF_002284575.1_ASM228457v1_genomic.fna/cds.fna -a GCF_002284575.1_ASM228457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:41,097] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:41,097] [INFO] Task started: HMMsearch
[2024-01-25 20:19:41,097] [INFO] Running command: hmmsearch --tblout GCF_002284575.1_ASM228457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/reference_markers.hmm GCF_002284575.1_ASM228457v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:41,414] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:41,415] [INFO] Found 6/6 markers.
[2024-01-25 20:19:41,467] [INFO] Query marker FASTA was written to GCF_002284575.1_ASM228457v1_genomic.fna/markers.fasta
[2024-01-25 20:19:41,468] [INFO] Task started: Blastn
[2024-01-25 20:19:41,468] [INFO] Running command: blastn -query GCF_002284575.1_ASM228457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/reference_markers.fasta -out GCF_002284575.1_ASM228457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:42,355] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:42,358] [INFO] Selected 16 target genomes.
[2024-01-25 20:19:42,358] [INFO] Target genome list was writen to GCF_002284575.1_ASM228457v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:42,370] [INFO] Task started: fastANI
[2024-01-25 20:19:42,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b5f9942-38f7-43d3-93da-d1addb2cb1f1/GCF_002284575.1_ASM228457v1_genomic.fna.gz --refList GCF_002284575.1_ASM228457v1_genomic.fna/target_genomes.txt --output GCF_002284575.1_ASM228457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:03,593] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:03,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:03,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:03,603] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:03,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:03,603] [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 temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	100.0	2340	2346	95	conclusive
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	94.787	1896	2346	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	93.2572	1748	2346	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.6916	1760	2346	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.5101	1400	2346	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	87.2624	1451	2346	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	87.2351	1274	2346	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.8645	1236	2346	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9922	689	2346	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.9855	690	2346	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9059	604	2346	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	75.5942	155	2346	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	75.2802	194	2346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:03,608] [INFO] DFAST Taxonomy check result was written to GCF_002284575.1_ASM228457v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:03,609] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:03,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:03,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/checkm_data
[2024-01-25 20:20:03,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:03,678] [INFO] Task started: CheckM
[2024-01-25 20:20:03,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002284575.1_ASM228457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002284575.1_ASM228457v1_genomic.fna/checkm_input GCF_002284575.1_ASM228457v1_genomic.fna/checkm_result
[2024-01-25 20:20:57,931] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:57,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:57,952] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:57,952] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:57,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002284575.1_ASM228457v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:57,953] [INFO] Task started: Blastn
[2024-01-25 20:20:57,953] [INFO] Running command: blastn -query GCF_002284575.1_ASM228457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2151c3d6-758f-4d48-acf1-a4e9eaecffbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002284575.1_ASM228457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:59,698] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:59,701] [INFO] Selected 14 target genomes.
[2024-01-25 20:20:59,701] [INFO] Target genome list was writen to GCF_002284575.1_ASM228457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:59,713] [INFO] Task started: fastANI
[2024-01-25 20:20:59,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b5f9942-38f7-43d3-93da-d1addb2cb1f1/GCF_002284575.1_ASM228457v1_genomic.fna.gz --refList GCF_002284575.1_ASM228457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002284575.1_ASM228457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:22,611] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:22,620] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:22,620] [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_002284575.1	s__Mesorhizobium temperatum	100.0	2340	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	conclusive
GCA_004020645.1	s__Mesorhizobium sp004020645	94.973	1880	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_002284535.1	s__Mesorhizobium wenxiniae	93.2466	1749	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	-
GCA_004020315.1	s__Mesorhizobium sp004020315	92.9358	1701	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCF_900156895.1	s__Mesorhizobium prunaredense	92.85	1732	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099905.1	s__Mesorhizobium muleiense	92.692	1759	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	-
GCA_004020365.1	s__Mesorhizobium sp004020365	92.5642	1729	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_016756595.1	s__Mesorhizobium sp004020105	92.1996	1761	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	92.0574	1698	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCA_004962925.1	s__Mesorhizobium sp004962925	91.9748	1496	2346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702655.1	s__CAIKUF01 sp016702655	75.4413	159	2346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	75.2776	195	2346	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:22,621] [INFO] GTDB search result was written to GCF_002284575.1_ASM228457v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:22,622] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:22,624] [INFO] DFAST_QC result json was written to GCF_002284575.1_ASM228457v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:22,625] [INFO] DFAST_QC completed!
[2024-01-25 20:21:22,625] [INFO] Total running time: 0h2m2s