[2024-01-24 11:26:54,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgef74ca5e-eb85-438c-8699-ed9904362788/GCF_002284535.1_ASM228453v1_genomic.fna.gz | prodigal -d GCF_002284535.1_ASM228453v1_genomic.fna/cds.fna -a GCF_002284535.1_ASM228453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:18,483] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:18,484] [INFO] Task started: HMMsearch
[2024-01-24 11:27:18,484] [INFO] Running command: hmmsearch --tblout GCF_002284535.1_ASM228453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/reference_markers.hmm GCF_002284535.1_ASM228453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:18,807] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:18,808] [INFO] Found 6/6 markers.
[2024-01-24 11:27:18,860] [INFO] Query marker FASTA was written to GCF_002284535.1_ASM228453v1_genomic.fna/markers.fasta
[2024-01-24 11:27:18,861] [INFO] Task started: Blastn
[2024-01-24 11:27:18,861] [INFO] Running command: blastn -query GCF_002284535.1_ASM228453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/reference_markers.fasta -out GCF_002284535.1_ASM228453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:19,933] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:19,937] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:19,938] [INFO] Target genome list was writen to GCF_002284535.1_ASM228453v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:19,946] [INFO] Task started: fastANI
[2024-01-24 11:27:19,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgef74ca5e-eb85-438c-8699-ed9904362788/GCF_002284535.1_ASM228453v1_genomic.fna.gz --refList GCF_002284535.1_ASM228453v1_genomic.fna/target_genomes.txt --output GCF_002284535.1_ASM228453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:37,312] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:37,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:37,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:37,326] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:37,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:37,326] [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 wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	100.0	2204	2206	95	conclusive
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	93.279	1728	2206	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	92.9108	1751	2206	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.782	1746	2206	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	87.14	1388	2206	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	86.9021	1418	2206	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.5264	1380	2206	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.8602	1231	2206	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.1654	604	2206	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.9103	693	2206	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.8726	699	2206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,328] [INFO] DFAST Taxonomy check result was written to GCF_002284535.1_ASM228453v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:37,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:37,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:37,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/checkm_data
[2024-01-24 11:27:37,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:37,393] [INFO] Task started: CheckM
[2024-01-24 11:27:37,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002284535.1_ASM228453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002284535.1_ASM228453v1_genomic.fna/checkm_input GCF_002284535.1_ASM228453v1_genomic.fna/checkm_result
[2024-01-24 11:28:33,678] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:33,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:33,703] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:33,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:33,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002284535.1_ASM228453v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:33,704] [INFO] Task started: Blastn
[2024-01-24 11:28:33,704] [INFO] Running command: blastn -query GCF_002284535.1_ASM228453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62478163-1636-4845-b55c-0463d10a1929/dqc_reference/reference_markers_gtdb.fasta -out GCF_002284535.1_ASM228453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:35,904] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:35,908] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:35,908] [INFO] Target genome list was writen to GCF_002284535.1_ASM228453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:35,915] [INFO] Task started: fastANI
[2024-01-24 11:28:35,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgef74ca5e-eb85-438c-8699-ed9904362788/GCF_002284535.1_ASM228453v1_genomic.fna.gz --refList GCF_002284535.1_ASM228453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002284535.1_ASM228453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:53,524] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:53,542] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:53,543] [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_002284535.1	s__Mesorhizobium wenxiniae	100.0	2204	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.50	95.53	0.83	0.79	62	conclusive
GCA_004020315.1	s__Mesorhizobium sp004020315	93.4394	1713	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.08	99.08	0.89	0.89	2	-
GCA_004020645.1	s__Mesorhizobium sp004020645	93.2924	1732	2206	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	93.2499	1731	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCF_900099905.1	s__Mesorhizobium muleiense	92.7924	1745	2206	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	92.5378	1700	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_900156895.1	s__Mesorhizobium prunaredense	92.1521	1665	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002284565.1	s__Mesorhizobium mediterraneum_A	92.1432	1716	2206	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	91.9887	1518	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756595.1	s__Mesorhizobium sp004020105	91.9205	1671	2206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.38	95.83	0.84	0.81	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:53,545] [INFO] GTDB search result was written to GCF_002284535.1_ASM228453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:53,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:53,549] [INFO] DFAST_QC result json was written to GCF_002284535.1_ASM228453v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:53,550] [INFO] DFAST_QC completed!
[2024-01-24 11:28:53,550] [INFO] Total running time: 0h1m59s