[2024-01-24 13:25:58,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,053] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference
[2024-01-24 13:26:00,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,374] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg71089948-cf2a-4f6a-a0f2-54922b4e9024/GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/cds.fna -a GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:20,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:20,253] [INFO] Task started: HMMsearch
[2024-01-24 13:26:20,253] [INFO] Running command: hmmsearch --tblout GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/reference_markers.hmm GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:20,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:20,635] [INFO] Found 6/6 markers.
[2024-01-24 13:26:20,689] [INFO] Query marker FASTA was written to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:26:20,689] [INFO] Task started: Blastn
[2024-01-24 13:26:20,689] [INFO] Running command: blastn -query GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/reference_markers.fasta -out GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:21,685] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:21,690] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:21,691] [INFO] Target genome list was writen to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:26:21,700] [INFO] Task started: fastANI
[2024-01-24 13:26:21,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg71089948-cf2a-4f6a-a0f2-54922b4e9024/GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna.gz --refList GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:41,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:41,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:41,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:41,886] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:41,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:41,887] [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 miluonense	strain=HAMBI 2971	GCA_900094545.1	411945	411945	type	True	100.0	2212	2217	95	conclusive
Rhizobium freirei	strain=PRF 81	GCA_000359745.1	1353277	1353277	type	True	91.4649	1739	2217	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	86.1974	1572	2217	95	below_threshold
Rhizobium hainanense	strain=CCBAU 57015	GCA_900094555.1	52131	52131	type	True	86.0918	1569	2217	95	below_threshold
Rhizobium tropici	strain=CIAT 899	GCA_000330885.1	398	398	type	True	85.7467	1432	2217	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	85.7133	1518	2217	95	below_threshold
Rhizobium lusitanum	strain=P1-7	GCA_900094565.1	293958	293958	suspected-type	True	85.6927	1481	2217	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	83.587	1257	2217	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	83.5337	1272	2217	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.5223	959	2217	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	80.4725	968	2217	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	79.5954	832	2217	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.3403	640	2217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:41,888] [INFO] DFAST Taxonomy check result was written to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:41,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:41,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:41,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/checkm_data
[2024-01-24 13:26:41,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:41,954] [INFO] Task started: CheckM
[2024-01-24 13:26:41,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/checkm_input GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:27:39,018] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:39,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:39,045] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:39,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:39,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:27:39,046] [INFO] Task started: Blastn
[2024-01-24 13:27:39,047] [INFO] Running command: blastn -query GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdbf806e-c14b-4f44-8add-2fe221425af6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:40,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:40,985] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:40,985] [INFO] Target genome list was writen to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:41,002] [INFO] Task started: fastANI
[2024-01-24 13:27:41,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg71089948-cf2a-4f6a-a0f2-54922b4e9024/GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna.gz --refList GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:09,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:09,241] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:09,242] [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_900094545.1	s__Rhizobium miluonense	100.0	2211	2217	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_000359745.1	s__Rhizobium freirei	91.4665	1739	2217	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	86.9289	1609	2217	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	86.5156	1492	2217	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	86.4556	1496	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641405.1	s__Rhizobium sp012641405	86.3122	1506	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.52	99.52	0.93	0.93	2	-
GCF_013322215.1	s__Rhizobium rhizogenes_D	86.2344	1576	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900094585.1	s__Rhizobium multihospitium	86.1974	1572	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.86	97.86	0.88	0.88	2	-
GCA_900469615.1	s__Rhizobium sp900469615	86.1828	1430	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.94	98.72	0.95	0.92	12	-
GCF_900094555.1	s__Rhizobium hainanense	86.0816	1570	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745735.1	s__Rhizobium rhizogenes_A	86.0782	1580	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472485.1	s__Rhizobium sp900472485	85.8826	1478	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.96	99.92	0.99	0.98	3	-
GCF_001692325.1	s__Rhizobium sp001692325	85.834	1515	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.36	95.29	0.93	0.90	3	-
GCF_000745725.1	s__Rhizobium rhizogenes_B	85.8259	1495	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469475.1	s__Rhizobium sp900469475	85.6978	1421	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.70	97.21	0.94	0.88	20	-
GCA_900469175.1	s__Rhizobium sp900469175	85.6804	1483	2217	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	95.56	0.94	0.85	48	-
GCF_012641435.1	s__Rhizobium sp012641435	84.7358	1392	2217	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	84.0376	1284	2217	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 13:28:09,244] [INFO] GTDB search result was written to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:09,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:09,251] [INFO] DFAST_QC result json was written to GCF_900094545.1_IMG-taxon_2617270742_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:28:09,251] [INFO] DFAST_QC completed!
[2024-01-24 13:28:09,252] [INFO] Total running time: 0h2m11s