[2024-01-25 20:27:05,563] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:05,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:05,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference
[2024-01-25 20:27:06,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:06,707] [INFO] Task started: Prodigal
[2024-01-25 20:27:06,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg581a6baa-4e43-4989-beef-f21924fd57f1/GCF_012927355.1_ASM1292735v1_genomic.fna.gz | prodigal -d GCF_012927355.1_ASM1292735v1_genomic.fna/cds.fna -a GCF_012927355.1_ASM1292735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:19,444] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:19,444] [INFO] Task started: HMMsearch
[2024-01-25 20:27:19,444] [INFO] Running command: hmmsearch --tblout GCF_012927355.1_ASM1292735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/reference_markers.hmm GCF_012927355.1_ASM1292735v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:19,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:19,755] [INFO] Found 6/6 markers.
[2024-01-25 20:27:19,795] [INFO] Query marker FASTA was written to GCF_012927355.1_ASM1292735v1_genomic.fna/markers.fasta
[2024-01-25 20:27:19,795] [INFO] Task started: Blastn
[2024-01-25 20:27:19,795] [INFO] Running command: blastn -query GCF_012927355.1_ASM1292735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/reference_markers.fasta -out GCF_012927355.1_ASM1292735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:20,783] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:20,786] [INFO] Selected 19 target genomes.
[2024-01-25 20:27:20,786] [INFO] Target genome list was writen to GCF_012927355.1_ASM1292735v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:20,812] [INFO] Task started: fastANI
[2024-01-25 20:27:20,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg581a6baa-4e43-4989-beef-f21924fd57f1/GCF_012927355.1_ASM1292735v1_genomic.fna.gz --refList GCF_012927355.1_ASM1292735v1_genomic.fna/target_genomes.txt --output GCF_012927355.1_ASM1292735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:41,847] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:41,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:41,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:41,860] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:27:41,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:27:41,860] [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
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	84.5735	1187	1634	95	below_threshold
Ciceribacter naphthalenivorans	strain=NBRC 107585	GCA_007992095.1	1118451	1118451	type	True	82.0396	974	1634	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	81.508	955	1634	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	81.4846	950	1634	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	81.4488	820	1634	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	81.3899	823	1634	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	81.2937	858	1634	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	81.1743	835	1634	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	81.1581	825	1634	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	81.0521	838	1634	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	80.7569	808	1634	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	80.3147	828	1634	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.1592	705	1634	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	80.0228	712	1634	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	79.9941	680	1634	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.7628	711	1634	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	79.2696	668	1634	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.012	359	1634	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.9737	369	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:41,861] [INFO] DFAST Taxonomy check result was written to GCF_012927355.1_ASM1292735v1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:41,862] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:41,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:41,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/checkm_data
[2024-01-25 20:27:41,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:41,910] [INFO] Task started: CheckM
[2024-01-25 20:27:41,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927355.1_ASM1292735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927355.1_ASM1292735v1_genomic.fna/checkm_input GCF_012927355.1_ASM1292735v1_genomic.fna/checkm_result
[2024-01-25 20:28:23,752] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:23,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:23,781] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:23,781] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:23,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927355.1_ASM1292735v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:23,782] [INFO] Task started: Blastn
[2024-01-25 20:28:23,782] [INFO] Running command: blastn -query GCF_012927355.1_ASM1292735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12daa2cc-2235-45b4-9692-9cc73d1b47c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927355.1_ASM1292735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:25,834] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:25,836] [INFO] Selected 13 target genomes.
[2024-01-25 20:28:25,836] [INFO] Target genome list was writen to GCF_012927355.1_ASM1292735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:25,847] [INFO] Task started: fastANI
[2024-01-25 20:28:25,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg581a6baa-4e43-4989-beef-f21924fd57f1/GCF_012927355.1_ASM1292735v1_genomic.fna.gz --refList GCF_012927355.1_ASM1292735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927355.1_ASM1292735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:40,205] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:40,213] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:40,214] [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_012927355.1	s__Allorhizobium sp012927355	100.0	1632	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002796995.1	s__Allorhizobium sp002796995	84.6234	1155	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_000518785.1	s__Allorhizobium selenitireducens	84.5843	1186	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	84.1725	1110	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCA_002307905.1	s__Allorhizobium sp002307905	82.6826	801	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992095.1	s__Allorhizobium naphthalenivorans	82.0608	972	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002600635.1	s__Allorhizobium sp002600635	82.0449	1001	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466005.1	s__Allorhizobium sp900466005	81.1945	842	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_003337715.1	s__Allorhizobium lividum	81.1538	826	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003527225.1	s__Allorhizobium sp003527225	81.0326	773	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706095.1	s__Allorhizobium sp902706095	80.9632	863	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017599385.1	s__Allorhizobium sp017599385	80.3409	745	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.20	97.20	0.96	0.96	2	-
GCA_017305935.1	s__Rhizobium sp017305935	80.0708	739	1634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:40,215] [INFO] GTDB search result was written to GCF_012927355.1_ASM1292735v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:40,216] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:40,219] [INFO] DFAST_QC result json was written to GCF_012927355.1_ASM1292735v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:40,219] [INFO] DFAST_QC completed!
[2024-01-25 20:28:40,219] [INFO] Total running time: 0h1m35s