[2023-06-04 19:37:49,554] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:37:49,556] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:37:49,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference
[2023-06-04 19:37:50,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:37:50,886] [INFO] Task started: Prodigal
[2023-06-04 19:37:50,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg531d9fa5-ea57-4a94-80ac-33d0acf86611/GCA_004021705.1_ASM402170v1_genomic.fna.gz | prodigal -d GCA_004021705.1_ASM402170v1_genomic.fna/cds.fna -a GCA_004021705.1_ASM402170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:12,475] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:12,476] [INFO] Task started: HMMsearch
[2023-06-04 19:38:12,476] [INFO] Running command: hmmsearch --tblout GCA_004021705.1_ASM402170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/reference_markers.hmm GCA_004021705.1_ASM402170v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:12,836] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:12,837] [INFO] Found 6/6 markers.
[2023-06-04 19:38:12,906] [INFO] Query marker FASTA was written to GCA_004021705.1_ASM402170v1_genomic.fna/markers.fasta
[2023-06-04 19:38:12,907] [INFO] Task started: Blastn
[2023-06-04 19:38:12,907] [INFO] Running command: blastn -query GCA_004021705.1_ASM402170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/reference_markers.fasta -out GCA_004021705.1_ASM402170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:14,025] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:14,032] [INFO] Selected 12 target genomes.
[2023-06-04 19:38:14,033] [INFO] Target genome list was writen to GCA_004021705.1_ASM402170v1_genomic.fna/target_genomes.txt
[2023-06-04 19:38:14,036] [INFO] Task started: fastANI
[2023-06-04 19:38:14,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg531d9fa5-ea57-4a94-80ac-33d0acf86611/GCA_004021705.1_ASM402170v1_genomic.fna.gz --refList GCA_004021705.1_ASM402170v1_genomic.fna/target_genomes.txt --output GCA_004021705.1_ASM402170v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:32,843] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:32,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:32,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:32,856] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 19:38:32,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 19:38:32,856] [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 muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	96.4008	1869	2336	95	conclusive
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	92.7246	1793	2336	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	92.6354	1830	2336	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	92.2381	1723	2336	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.2706	1361	2336	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	87.0955	1396	2336	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	86.8465	1272	2336	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	84.7872	1258	2336	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.967	1188	2336	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.0621	676	2336	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.0504	679	2336	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9772	602	2336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 19:38:32,861] [INFO] DFAST Taxonomy check result was written to GCA_004021705.1_ASM402170v1_genomic.fna/tc_result.tsv
[2023-06-04 19:38:32,861] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:32,862] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:32,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/checkm_data
[2023-06-04 19:38:32,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:32,932] [INFO] Task started: CheckM
[2023-06-04 19:38:32,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004021705.1_ASM402170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004021705.1_ASM402170v1_genomic.fna/checkm_input GCA_004021705.1_ASM402170v1_genomic.fna/checkm_result
[2023-06-04 19:39:34,513] [INFO] Task succeeded: CheckM
[2023-06-04 19:39:34,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:39:34,537] [INFO] ===== Completeness check finished =====
[2023-06-04 19:39:34,537] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:39:34,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004021705.1_ASM402170v1_genomic.fna/markers.fasta)
[2023-06-04 19:39:34,538] [INFO] Task started: Blastn
[2023-06-04 19:39:34,538] [INFO] Running command: blastn -query GCA_004021705.1_ASM402170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d5b8b1e-8d3c-412c-ad7b-87972f7863e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_004021705.1_ASM402170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:39:36,693] [INFO] Task succeeded: Blastn
[2023-06-04 19:39:36,699] [INFO] Selected 7 target genomes.
[2023-06-04 19:39:36,699] [INFO] Target genome list was writen to GCA_004021705.1_ASM402170v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:39:36,701] [INFO] Task started: fastANI
[2023-06-04 19:39:36,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg531d9fa5-ea57-4a94-80ac-33d0acf86611/GCA_004021705.1_ASM402170v1_genomic.fna.gz --refList GCA_004021705.1_ASM402170v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004021705.1_ASM402170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:39:51,078] [INFO] Task succeeded: fastANI
[2023-06-04 19:39:51,089] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:39:51,089] [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_900099905.1	s__Mesorhizobium muleiense	96.4008	1869	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.77	96.33	0.85	0.80	57	conclusive
GCF_900156895.1	s__Mesorhizobium prunaredense	94.8157	1812	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020365.1	s__Mesorhizobium sp004020365	94.4175	1769	2336	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	93.9561	1819	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
GCA_004020645.1	s__Mesorhizobium sp004020645	93.6505	1879	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCF_002284575.1	s__Mesorhizobium temperatum	92.7231	1793	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCA_004020315.1	s__Mesorhizobium sp004020315	92.3783	1697	2336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-04 19:39:51,091] [INFO] GTDB search result was written to GCA_004021705.1_ASM402170v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:39:51,092] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:39:51,095] [INFO] DFAST_QC result json was written to GCA_004021705.1_ASM402170v1_genomic.fna/dqc_result.json
[2023-06-04 19:39:51,096] [INFO] DFAST_QC completed!
[2023-06-04 19:39:51,096] [INFO] Total running time: 0h2m2s