[2024-01-24 13:55:28,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:28,190] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:28,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference
[2024-01-24 13:55:29,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:29,378] [INFO] Task started: Prodigal
[2024-01-24 13:55:29,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b940918-d764-4151-a112-7afd33a90728/GCF_009176305.1_ASM917630v1_genomic.fna.gz | prodigal -d GCF_009176305.1_ASM917630v1_genomic.fna/cds.fna -a GCF_009176305.1_ASM917630v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:49,587] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:49,587] [INFO] Task started: HMMsearch
[2024-01-24 13:55:49,587] [INFO] Running command: hmmsearch --tblout GCF_009176305.1_ASM917630v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/reference_markers.hmm GCF_009176305.1_ASM917630v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:49,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:49,853] [INFO] Found 6/6 markers.
[2024-01-24 13:55:49,903] [INFO] Query marker FASTA was written to GCF_009176305.1_ASM917630v1_genomic.fna/markers.fasta
[2024-01-24 13:55:49,903] [INFO] Task started: Blastn
[2024-01-24 13:55:49,903] [INFO] Running command: blastn -query GCF_009176305.1_ASM917630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/reference_markers.fasta -out GCF_009176305.1_ASM917630v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:50,883] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:50,886] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:50,887] [INFO] Target genome list was writen to GCF_009176305.1_ASM917630v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:50,895] [INFO] Task started: fastANI
[2024-01-24 13:55:50,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b940918-d764-4151-a112-7afd33a90728/GCF_009176305.1_ASM917630v1_genomic.fna.gz --refList GCF_009176305.1_ASM917630v1_genomic.fna/target_genomes.txt --output GCF_009176305.1_ASM917630v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:07,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:07,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:07,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:07,922] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:07,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:07,922] [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 dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	100.0	2213	2216	95	conclusive
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	91.2633	1892	2216	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	89.6578	1692	2216	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	89.3897	1877	2216	95	below_threshold
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	85.9296	1502	2216	95	below_threshold
Rhizobium miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	85.6655	1531	2216	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	84.7918	1536	2216	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.4815	975	2216	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.3761	995	2216	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.4598	828	2216	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.2094	671	2216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:07,923] [INFO] DFAST Taxonomy check result was written to GCF_009176305.1_ASM917630v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:07,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:07,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:07,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/checkm_data
[2024-01-24 13:56:07,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:07,984] [INFO] Task started: CheckM
[2024-01-24 13:56:07,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009176305.1_ASM917630v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009176305.1_ASM917630v1_genomic.fna/checkm_input GCF_009176305.1_ASM917630v1_genomic.fna/checkm_result
[2024-01-24 13:57:04,771] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,795] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,795] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009176305.1_ASM917630v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,796] [INFO] Task started: Blastn
[2024-01-24 13:57:04,796] [INFO] Running command: blastn -query GCF_009176305.1_ASM917630v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg328dd48e-f31c-45de-a7a9-217741fa9a3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009176305.1_ASM917630v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,712] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,716] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:06,716] [INFO] Target genome list was writen to GCF_009176305.1_ASM917630v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:06,734] [INFO] Task started: fastANI
[2024-01-24 13:57:06,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b940918-d764-4151-a112-7afd33a90728/GCF_009176305.1_ASM917630v1_genomic.fna.gz --refList GCF_009176305.1_ASM917630v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009176305.1_ASM917630v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:23,975] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:23,985] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:23,985] [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
GCA_900469175.1	s__Rhizobium sp900469175	98.2521	2010	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	95.56	0.94	0.85	48	conclusive
GCF_002277895.1	s__Rhizobium sp002277895	93.3371	1981	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.72	98.72	0.92	0.92	2	-
GCA_900472485.1	s__Rhizobium sp900472485	91.8093	1879	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.96	99.92	0.99	0.98	3	-
GCF_900094585.1	s__Rhizobium multihospitium	91.2633	1892	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.86	97.86	0.88	0.88	2	-
GCA_900469475.1	s__Rhizobium sp900469475	89.8634	1736	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.70	97.21	0.94	0.88	20	-
GCF_003024605.1	s__Rhizobium sp003024605	89.676	1237	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.03	99.00	0.96	0.95	8	-
GCF_900094555.1	s__Rhizobium hainanense	89.3897	1877	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829155.1	s__Rhizobium sp900467885	88.7561	1716	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.99	98.86	0.92	0.89	10	-
GCA_900468625.1	s__Rhizobium sp900468625	87.4538	1611	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.33	98.37	0.95	0.89	8	-
GCF_010668395.1	s__Rhizobium lusitanum_A	86.7051	1558	2216	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359745.1	s__Rhizobium freirei	85.9199	1504	2216	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 13:57:23,987] [INFO] GTDB search result was written to GCF_009176305.1_ASM917630v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:23,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:23,991] [INFO] DFAST_QC result json was written to GCF_009176305.1_ASM917630v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:23,991] [INFO] DFAST_QC completed!
[2024-01-24 13:57:23,991] [INFO] Total running time: 0h1m56s