[2023-06-05 18:05:29,308] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:29,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:29,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference
[2023-06-05 18:05:30,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:30,758] [INFO] Task started: Prodigal
[2023-06-05 18:05:30,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1301062-11cb-4ea1-9c5d-a6c4bd9f0b1b/GCA_004965005.1_ASM496500v1_genomic.fna.gz | prodigal -d GCA_004965005.1_ASM496500v1_genomic.fna/cds.fna -a GCA_004965005.1_ASM496500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:05:53,989] [INFO] Task succeeded: Prodigal
[2023-06-05 18:05:53,990] [INFO] Task started: HMMsearch
[2023-06-05 18:05:53,990] [INFO] Running command: hmmsearch --tblout GCA_004965005.1_ASM496500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/reference_markers.hmm GCA_004965005.1_ASM496500v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:05:54,723] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:05:54,724] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc1301062-11cb-4ea1-9c5d-a6c4bd9f0b1b/GCA_004965005.1_ASM496500v1_genomic.fna.gz]
[2023-06-05 18:05:54,845] [INFO] Query marker FASTA was written to GCA_004965005.1_ASM496500v1_genomic.fna/markers.fasta
[2023-06-05 18:05:54,845] [INFO] Task started: Blastn
[2023-06-05 18:05:54,846] [INFO] Running command: blastn -query GCA_004965005.1_ASM496500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/reference_markers.fasta -out GCA_004965005.1_ASM496500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:57,660] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:57,679] [INFO] Selected 13 target genomes.
[2023-06-05 18:05:57,680] [INFO] Target genome list was writen to GCA_004965005.1_ASM496500v1_genomic.fna/target_genomes.txt
[2023-06-05 18:05:57,681] [INFO] Task started: fastANI
[2023-06-05 18:05:57,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1301062-11cb-4ea1-9c5d-a6c4bd9f0b1b/GCA_004965005.1_ASM496500v1_genomic.fna.gz --refList GCA_004965005.1_ASM496500v1_genomic.fna/target_genomes.txt --output GCA_004965005.1_ASM496500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:06:18,310] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:18,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:06:18,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:06:18,322] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 18:06:18,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:06:18,323] [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	97.1178	644	810	95	conclusive
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	92.1682	597	810	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	91.791	552	810	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	91.5652	564	810	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	85.8052	408	810	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	85.7437	427	810	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	84.7569	414	810	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	84.336	396	810	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	83.4785	393	810	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	83.0863	323	810	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.1975	196	810	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.1871	157	810	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0853	171	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:06:18,340] [INFO] DFAST Taxonomy check result was written to GCA_004965005.1_ASM496500v1_genomic.fna/tc_result.tsv
[2023-06-05 18:06:18,340] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:06:18,340] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:06:18,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/checkm_data
[2023-06-05 18:06:18,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:06:18,397] [INFO] Task started: CheckM
[2023-06-05 18:06:18,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004965005.1_ASM496500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004965005.1_ASM496500v1_genomic.fna/checkm_input GCA_004965005.1_ASM496500v1_genomic.fna/checkm_result
[2023-06-05 18:07:22,859] [INFO] Task succeeded: CheckM
[2023-06-05 18:07:22,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:07:22,887] [INFO] ===== Completeness check finished =====
[2023-06-05 18:07:22,887] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:07:22,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004965005.1_ASM496500v1_genomic.fna/markers.fasta)
[2023-06-05 18:07:22,888] [INFO] Task started: Blastn
[2023-06-05 18:07:22,888] [INFO] Running command: blastn -query GCA_004965005.1_ASM496500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d6f2a45-aeb5-430f-98ec-48fce97b7327/dqc_reference/reference_markers_gtdb.fasta -out GCA_004965005.1_ASM496500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:07:24,934] [INFO] Task succeeded: Blastn
[2023-06-05 18:07:24,939] [INFO] Selected 8 target genomes.
[2023-06-05 18:07:24,939] [INFO] Target genome list was writen to GCA_004965005.1_ASM496500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:07:24,940] [INFO] Task started: fastANI
[2023-06-05 18:07:24,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1301062-11cb-4ea1-9c5d-a6c4bd9f0b1b/GCA_004965005.1_ASM496500v1_genomic.fna.gz --refList GCA_004965005.1_ASM496500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004965005.1_ASM496500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:07:34,942] [INFO] Task succeeded: fastANI
[2023-06-05 18:07:34,950] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:07:34,950] [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	97.1178	644	810	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	92.6381	579	810	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	92.0832	581	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.46	97.82	0.90	0.85	20	-
GCA_004020365.1	s__Mesorhizobium sp004020365	91.8116	593	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.10	96.06	0.82	0.80	8	-
GCF_002284575.1	s__Mesorhizobium temperatum	91.791	552	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.74	95.09	0.81	0.81	3	-
GCA_004962925.1	s__Mesorhizobium sp004962925	91.4045	532	810	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	91.2983	555	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.16	97.72	0.92	0.89	20	-
GCF_900156895.1	s__Mesorhizobium prunaredense	90.3435	535	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:07:34,952] [INFO] GTDB search result was written to GCA_004965005.1_ASM496500v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:07:34,953] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:07:34,957] [INFO] DFAST_QC result json was written to GCA_004965005.1_ASM496500v1_genomic.fna/dqc_result.json
[2023-06-05 18:07:34,957] [INFO] DFAST_QC completed!
[2023-06-05 18:07:34,957] [INFO] Total running time: 0h2m6s