[2024-01-25 20:12:50,492] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:50,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:50,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference
[2024-01-25 20:12:51,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:51,656] [INFO] Task started: Prodigal
[2024-01-25 20:12:51,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg938066d9-e66e-4ffe-a4a9-0f7229752e21/GCF_003289965.1_ASM328996v1_genomic.fna.gz | prodigal -d GCF_003289965.1_ASM328996v1_genomic.fna/cds.fna -a GCF_003289965.1_ASM328996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:09,347] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:09,347] [INFO] Task started: HMMsearch
[2024-01-25 20:13:09,347] [INFO] Running command: hmmsearch --tblout GCF_003289965.1_ASM328996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/reference_markers.hmm GCF_003289965.1_ASM328996v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:09,679] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:09,680] [INFO] Found 6/6 markers.
[2024-01-25 20:13:09,736] [INFO] Query marker FASTA was written to GCF_003289965.1_ASM328996v1_genomic.fna/markers.fasta
[2024-01-25 20:13:09,736] [INFO] Task started: Blastn
[2024-01-25 20:13:09,736] [INFO] Running command: blastn -query GCF_003289965.1_ASM328996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/reference_markers.fasta -out GCF_003289965.1_ASM328996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:10,788] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:10,792] [INFO] Selected 15 target genomes.
[2024-01-25 20:13:10,792] [INFO] Target genome list was writen to GCF_003289965.1_ASM328996v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:10,804] [INFO] Task started: fastANI
[2024-01-25 20:13:10,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg938066d9-e66e-4ffe-a4a9-0f7229752e21/GCF_003289965.1_ASM328996v1_genomic.fna.gz --refList GCF_003289965.1_ASM328996v1_genomic.fna/target_genomes.txt --output GCF_003289965.1_ASM328996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:35,387] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:35,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:35,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:35,398] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:35,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:35,398] [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 atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	100.0	2163	2165	95	conclusive
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	89.8576	1721	2165	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	87.2342	1551	2165	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	87.2143	1444	2165	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	84.8519	1485	2165	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	84.7791	1419	2165	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.3311	1405	2165	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.3167	1251	2165	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	84.2026	1218	2165	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	84.195	1475	2165	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	84.1567	1360	2165	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.4671	1269	2165	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.2874	732	2165	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.2717	736	2165	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	79.1451	634	2165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:35,399] [INFO] DFAST Taxonomy check result was written to GCF_003289965.1_ASM328996v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:35,400] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:35,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:35,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/checkm_data
[2024-01-25 20:13:35,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:35,460] [INFO] Task started: CheckM
[2024-01-25 20:13:35,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003289965.1_ASM328996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003289965.1_ASM328996v1_genomic.fna/checkm_input GCF_003289965.1_ASM328996v1_genomic.fna/checkm_result
[2024-01-25 20:14:25,671] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:25,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:25,695] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:25,696] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:25,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003289965.1_ASM328996v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:25,697] [INFO] Task started: Blastn
[2024-01-25 20:14:25,697] [INFO] Running command: blastn -query GCF_003289965.1_ASM328996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca3031a-756f-4188-895d-15bdcd4587e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003289965.1_ASM328996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:27,918] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:27,921] [INFO] Selected 11 target genomes.
[2024-01-25 20:14:27,921] [INFO] Target genome list was writen to GCF_003289965.1_ASM328996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:27,927] [INFO] Task started: fastANI
[2024-01-25 20:14:27,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg938066d9-e66e-4ffe-a4a9-0f7229752e21/GCF_003289965.1_ASM328996v1_genomic.fna.gz --refList GCF_003289965.1_ASM328996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003289965.1_ASM328996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:49,489] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:49,497] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:49,497] [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_003289965.1	s__Mesorhizobium atlanticum	100.0	2163	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004016445.2	s__Mesorhizobium sp004016445	93.6485	1763	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_002295065.1	s__Mesorhizobium sp002295065	93.1882	1702	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952425.1	s__Mesorhizobium sp003952425	92.4032	1704	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCA_000824845.1	s__Mesorhizobium sp000824845	92.2703	1672	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004017535.1	s__Mesorhizobium sp004017535	92.1565	1685	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.05	98.03	0.89	0.85	7	-
GCA_004020875.1	s__Mesorhizobium sp004020875	91.7957	1670	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.89	99.01	0.98	0.89	11	-
GCA_000824785.1	s__Mesorhizobium plurifarium	90.7409	1731	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCF_019091085.1	s__Mesorhizobium sp019091085	90.563	1665	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	90.3348	1582	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440775.1	s__Mesorhizobium sp006440775	89.7461	1580	2165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.82	97.16	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:49,498] [INFO] GTDB search result was written to GCF_003289965.1_ASM328996v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:49,499] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:49,502] [INFO] DFAST_QC result json was written to GCF_003289965.1_ASM328996v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:49,502] [INFO] DFAST_QC completed!
[2024-01-25 20:14:49,502] [INFO] Total running time: 0h1m59s