[2024-01-24 14:13:18,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference
[2024-01-24 14:13:19,994] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:19,995] [INFO] Task started: Prodigal
[2024-01-24 14:13:19,995] [INFO] Running command: gunzip -c /var/lib/cwl/stgca0d8442-8e93-471c-8e15-c4ff6fc6307e/GCF_000359745.1_Rhizobium_sp._genomic.fna.gz | prodigal -d GCF_000359745.1_Rhizobium_sp._genomic.fna/cds.fna -a GCF_000359745.1_Rhizobium_sp._genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:40,852] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:40,853] [INFO] Task started: HMMsearch
[2024-01-24 14:13:40,853] [INFO] Running command: hmmsearch --tblout GCF_000359745.1_Rhizobium_sp._genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/reference_markers.hmm GCF_000359745.1_Rhizobium_sp._genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:41,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:41,237] [INFO] Found 6/6 markers.
[2024-01-24 14:13:41,313] [INFO] Query marker FASTA was written to GCF_000359745.1_Rhizobium_sp._genomic.fna/markers.fasta
[2024-01-24 14:13:41,313] [INFO] Task started: Blastn
[2024-01-24 14:13:41,313] [INFO] Running command: blastn -query GCF_000359745.1_Rhizobium_sp._genomic.fna/markers.fasta -db /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/reference_markers.fasta -out GCF_000359745.1_Rhizobium_sp._genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:42,392] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:42,396] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:42,396] [INFO] Target genome list was writen to GCF_000359745.1_Rhizobium_sp._genomic.fna/target_genomes.txt
[2024-01-24 14:13:42,402] [INFO] Task started: fastANI
[2024-01-24 14:13:42,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0d8442-8e93-471c-8e15-c4ff6fc6307e/GCF_000359745.1_Rhizobium_sp._genomic.fna.gz --refList GCF_000359745.1_Rhizobium_sp._genomic.fna/target_genomes.txt --output GCF_000359745.1_Rhizobium_sp._genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:00,329] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:00,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:00,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:00,345] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:00,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:00,346] [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
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	100.0	2330	2331	95	conclusive
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	91.4595	1742	2331	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	87.7557	1604	2331	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	87.488	1657	2331	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	86.4712	1562	2331	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	86.3182	1566	2331	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	85.9644	1505	2331	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.895	994	2331	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.8453	1018	2331	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.6278	857	2331	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.8592	629	2331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:00,355] [INFO] DFAST Taxonomy check result was written to GCF_000359745.1_Rhizobium_sp._genomic.fna/tc_result.tsv
[2024-01-24 14:14:00,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:00,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:00,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/checkm_data
[2024-01-24 14:14:00,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:00,429] [INFO] Task started: CheckM
[2024-01-24 14:14:00,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000359745.1_Rhizobium_sp._genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000359745.1_Rhizobium_sp._genomic.fna/checkm_input GCF_000359745.1_Rhizobium_sp._genomic.fna/checkm_result
[2024-01-24 14:14:59,919] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:59,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:59,946] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:59,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:59,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000359745.1_Rhizobium_sp._genomic.fna/markers.fasta)
[2024-01-24 14:14:59,948] [INFO] Task started: Blastn
[2024-01-24 14:14:59,948] [INFO] Running command: blastn -query GCF_000359745.1_Rhizobium_sp._genomic.fna/markers.fasta -db /var/lib/cwl/stg55be4b38-6a15-4d46-b24e-b764f91c0d44/dqc_reference/reference_markers_gtdb.fasta -out GCF_000359745.1_Rhizobium_sp._genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:01,897] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:01,900] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:01,901] [INFO] Target genome list was writen to GCF_000359745.1_Rhizobium_sp._genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:01,912] [INFO] Task started: fastANI
[2024-01-24 14:15:01,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0d8442-8e93-471c-8e15-c4ff6fc6307e/GCF_000359745.1_Rhizobium_sp._genomic.fna.gz --refList GCF_000359745.1_Rhizobium_sp._genomic.fna/target_genomes_gtdb.txt --output GCF_000359745.1_Rhizobium_sp._genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:24,145] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:24,158] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:24,159] [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_000359745.1	s__Rhizobium freirei	100.0	2330	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900094545.1	s__Rhizobium miluonense	91.4414	1744	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207095.1	s__Rhizobium lusitanum_B	88.622	1749	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627795.1	s__Rhizobium sp003627795	87.7941	1662	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.80	99.80	0.98	0.98	2	-
GCF_010668395.1	s__Rhizobium lusitanum_A	86.591	1474	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024605.1	s__Rhizobium sp003024605	86.4894	1128	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.03	99.00	0.96	0.95	8	-
GCF_900094585.1	s__Rhizobium multihospitium	86.4787	1561	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.86	97.86	0.88	0.88	2	-
GCF_013322215.1	s__Rhizobium rhizogenes_D	86.419	1571	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900469615.1	s__Rhizobium sp900469615	86.2799	1444	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.94	98.72	0.95	0.92	12	-
GCF_000799755.1	s__Rhizobium tropici_A	86.2417	1521	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.89	99.82	0.97	0.95	4	-
GCA_900472485.1	s__Rhizobium sp900472485	86.121	1483	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.96	99.92	0.99	0.98	3	-
GCF_000745735.1	s__Rhizobium rhizogenes_A	85.9774	1552	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641435.1	s__Rhizobium sp012641435	85.0374	1376	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	84.4469	1286	2331	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:24,161] [INFO] GTDB search result was written to GCF_000359745.1_Rhizobium_sp._genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:24,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:24,165] [INFO] DFAST_QC result json was written to GCF_000359745.1_Rhizobium_sp._genomic.fna/dqc_result.json
[2024-01-24 14:15:24,165] [INFO] DFAST_QC completed!
[2024-01-24 14:15:24,165] [INFO] Total running time: 0h2m6s