[2024-01-24 13:21:11,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference
[2024-01-24 13:21:12,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,461] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg256c081f-7624-4c42-bfaa-6ed672b7cd6d/GCF_013087605.1_ASM1308760v1_genomic.fna.gz | prodigal -d GCF_013087605.1_ASM1308760v1_genomic.fna/cds.fna -a GCF_013087605.1_ASM1308760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:33,946] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:33,947] [INFO] Task started: HMMsearch
[2024-01-24 13:21:33,947] [INFO] Running command: hmmsearch --tblout GCF_013087605.1_ASM1308760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/reference_markers.hmm GCF_013087605.1_ASM1308760v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:34,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:34,283] [INFO] Found 6/6 markers.
[2024-01-24 13:21:34,344] [INFO] Query marker FASTA was written to GCF_013087605.1_ASM1308760v1_genomic.fna/markers.fasta
[2024-01-24 13:21:34,344] [INFO] Task started: Blastn
[2024-01-24 13:21:34,344] [INFO] Running command: blastn -query GCF_013087605.1_ASM1308760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/reference_markers.fasta -out GCF_013087605.1_ASM1308760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:35,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:35,333] [INFO] Selected 13 target genomes.
[2024-01-24 13:21:35,333] [INFO] Target genome list was writen to GCF_013087605.1_ASM1308760v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:35,341] [INFO] Task started: fastANI
[2024-01-24 13:21:35,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg256c081f-7624-4c42-bfaa-6ed672b7cd6d/GCF_013087605.1_ASM1308760v1_genomic.fna.gz --refList GCF_013087605.1_ASM1308760v1_genomic.fna/target_genomes.txt --output GCF_013087605.1_ASM1308760v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:58,298] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:58,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:58,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:58,311] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:21:58,312] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:21:58,312] [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 indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	100.0	2456	2457	95	inconclusive
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	97.7575	2151	2457	95	inconclusive
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	97.7507	2147	2457	95	inconclusive
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	97.7033	2159	2457	95	inconclusive
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	93.2864	2006	2457	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	92.8848	1964	2457	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	92.4731	1912	2457	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	92.4499	1808	2457	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.0498	1755	2457	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.0161	1637	2457	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.6396	1241	2457	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.1451	1037	2457	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.971	721	2457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:58,314] [INFO] DFAST Taxonomy check result was written to GCF_013087605.1_ASM1308760v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:58,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:58,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:58,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/checkm_data
[2024-01-24 13:21:58,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:58,400] [INFO] Task started: CheckM
[2024-01-24 13:21:58,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013087605.1_ASM1308760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013087605.1_ASM1308760v1_genomic.fna/checkm_input GCF_013087605.1_ASM1308760v1_genomic.fna/checkm_result
[2024-01-24 13:23:01,088] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:01,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:01,119] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:01,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013087605.1_ASM1308760v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:01,119] [INFO] Task started: Blastn
[2024-01-24 13:23:01,120] [INFO] Running command: blastn -query GCF_013087605.1_ASM1308760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a302a8f-0517-432c-80c8-4f6abc790566/dqc_reference/reference_markers_gtdb.fasta -out GCF_013087605.1_ASM1308760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:03,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:03,167] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:03,167] [INFO] Target genome list was writen to GCF_013087605.1_ASM1308760v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:03,193] [INFO] Task started: fastANI
[2024-01-24 13:23:03,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg256c081f-7624-4c42-bfaa-6ed672b7cd6d/GCF_013087605.1_ASM1308760v1_genomic.fna.gz --refList GCF_013087605.1_ASM1308760v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013087605.1_ASM1308760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:22,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:22,073] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:22,074] [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_002008365.1	s__Rhizobium leguminosarum	97.7615	2146	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	conclusive
GCF_002953715.1	s__Rhizobium leguminosarum_K	94.5773	2091	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_001657485.1	s__Rhizobium sp001657485	93.3899	1960	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	93.3251	1921	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	93.2956	2005	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_005862305.2	s__Rhizobium indicum	92.8848	1964	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.44	95.15	0.91	0.82	6	-
GCF_004123835.1	s__Rhizobium leguminosarum_M	92.7268	1876	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023185.1	s__Rhizobium leguminosarum_J	92.6775	1911	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	97.68	0.92	0.88	6	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	92.6119	1963	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_013087515.1	s__Rhizobium sophorae	92.4599	1914	2457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,075] [INFO] GTDB search result was written to GCF_013087605.1_ASM1308760v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:22,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:22,081] [INFO] DFAST_QC result json was written to GCF_013087605.1_ASM1308760v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:22,081] [INFO] DFAST_QC completed!
[2024-01-24 13:23:22,082] [INFO] Total running time: 0h2m11s