[2024-01-24 11:52:48,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:48,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:48,218] [INFO] DQC Reference Directory: /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference
[2024-01-24 11:52:49,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:49,461] [INFO] Task started: Prodigal
[2024-01-24 11:52:49,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg83c271db-2ca6-48a0-90af-b3caf2cff431/GCF_014202175.1_ASM1420217v1_genomic.fna.gz | prodigal -d GCF_014202175.1_ASM1420217v1_genomic.fna/cds.fna -a GCF_014202175.1_ASM1420217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:53:03,815] [INFO] Task succeeded: Prodigal
[2024-01-24 11:53:03,815] [INFO] Task started: HMMsearch
[2024-01-24 11:53:03,816] [INFO] Running command: hmmsearch --tblout GCF_014202175.1_ASM1420217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/reference_markers.hmm GCF_014202175.1_ASM1420217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:53:04,115] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:53:04,117] [INFO] Found 6/6 markers.
[2024-01-24 11:53:04,168] [INFO] Query marker FASTA was written to GCF_014202175.1_ASM1420217v1_genomic.fna/markers.fasta
[2024-01-24 11:53:04,169] [INFO] Task started: Blastn
[2024-01-24 11:53:04,169] [INFO] Running command: blastn -query GCF_014202175.1_ASM1420217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/reference_markers.fasta -out GCF_014202175.1_ASM1420217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:05,174] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:05,178] [INFO] Selected 12 target genomes.
[2024-01-24 11:53:05,179] [INFO] Target genome list was writen to GCF_014202175.1_ASM1420217v1_genomic.fna/target_genomes.txt
[2024-01-24 11:53:05,184] [INFO] Task started: fastANI
[2024-01-24 11:53:05,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c271db-2ca6-48a0-90af-b3caf2cff431/GCF_014202175.1_ASM1420217v1_genomic.fna.gz --refList GCF_014202175.1_ASM1420217v1_genomic.fna/target_genomes.txt --output GCF_014202175.1_ASM1420217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:17,989] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:17,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:17,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:18,005] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:53:18,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:18,005] [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 rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	100.0	1622	1625	95	conclusive
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	99.9769	1602	1625	95	conclusive
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	85.7422	1189	1625	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	84.2461	1059	1625	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	83.9237	1061	1625	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	80.357	694	1625	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	80.1942	731	1625	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.8379	675	1625	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.4719	585	1625	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	79.3073	606	1625	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	78.7548	547	1625	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.9733	401	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:18,007] [INFO] DFAST Taxonomy check result was written to GCF_014202175.1_ASM1420217v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:18,007] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:18,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:18,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/checkm_data
[2024-01-24 11:53:18,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:18,053] [INFO] Task started: CheckM
[2024-01-24 11:53:18,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202175.1_ASM1420217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202175.1_ASM1420217v1_genomic.fna/checkm_input GCF_014202175.1_ASM1420217v1_genomic.fna/checkm_result
[2024-01-24 11:54:01,413] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:01,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:01,432] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:01,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:01,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202175.1_ASM1420217v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:01,434] [INFO] Task started: Blastn
[2024-01-24 11:54:01,434] [INFO] Running command: blastn -query GCF_014202175.1_ASM1420217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00b9b057-1c88-4215-8705-d8f7d62353fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202175.1_ASM1420217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:03,450] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:03,454] [INFO] Selected 13 target genomes.
[2024-01-24 11:54:03,454] [INFO] Target genome list was writen to GCF_014202175.1_ASM1420217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:03,494] [INFO] Task started: fastANI
[2024-01-24 11:54:03,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c271db-2ca6-48a0-90af-b3caf2cff431/GCF_014202175.1_ASM1420217v1_genomic.fna.gz --refList GCF_014202175.1_ASM1420217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202175.1_ASM1420217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:18,144] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:18,162] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:18,162] [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_004912135.1	s__Allorhizobium rosettiformans	99.9769	1602	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	conclusive
GCF_002855515.1	s__Allorhizobium sp002855515	86.7256	1237	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237835.1	s__Allorhizobium sp014237835	86.1924	1184	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300855.1	s__Allorhizobium albertimagni	86.0626	1206	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806065.1	s__Allorhizobium sp001724035	86.0179	1207	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCF_001713475.1	s__Allorhizobium sp001713475	85.9979	1212	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCF_900156055.1	s__Allorhizobium sp900156055	85.9188	1201	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912145.1	s__Allorhizobium rhizophilum	85.7471	1188	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
GCA_900473805.1	s__Allorhizobium sp900473805	85.287	1095	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.45	97.28	0.98	0.92	6	-
GCF_003205195.1	s__Allorhizobium wuzhouense	84.2301	1061	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCF_006443685.1	s__Allorhizobium glycinendophyticum	83.9248	1062	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429245.1	s__Allorhizobium sp001429245	83.7816	1034	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017599385.1	s__Allorhizobium sp017599385	80.8936	731	1625	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.20	97.20	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:18,163] [INFO] GTDB search result was written to GCF_014202175.1_ASM1420217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:18,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:18,167] [INFO] DFAST_QC result json was written to GCF_014202175.1_ASM1420217v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:18,167] [INFO] DFAST_QC completed!
[2024-01-24 11:54:18,167] [INFO] Total running time: 0h1m30s