[2024-01-24 12:37:07,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:07,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:07,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference
[2024-01-24 12:37:08,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:08,574] [INFO] Task started: Prodigal
[2024-01-24 12:37:08,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a519931-0149-4f4d-bccf-2fdb653a2d55/GCF_019684455.1_ASM1968445v1_genomic.fna.gz | prodigal -d GCF_019684455.1_ASM1968445v1_genomic.fna/cds.fna -a GCF_019684455.1_ASM1968445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:29,135] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:29,136] [INFO] Task started: HMMsearch
[2024-01-24 12:37:29,136] [INFO] Running command: hmmsearch --tblout GCF_019684455.1_ASM1968445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/reference_markers.hmm GCF_019684455.1_ASM1968445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:29,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:29,479] [INFO] Found 6/6 markers.
[2024-01-24 12:37:29,533] [INFO] Query marker FASTA was written to GCF_019684455.1_ASM1968445v1_genomic.fna/markers.fasta
[2024-01-24 12:37:29,534] [INFO] Task started: Blastn
[2024-01-24 12:37:29,534] [INFO] Running command: blastn -query GCF_019684455.1_ASM1968445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/reference_markers.fasta -out GCF_019684455.1_ASM1968445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:30,555] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:30,559] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:30,560] [INFO] Target genome list was writen to GCF_019684455.1_ASM1968445v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:30,569] [INFO] Task started: fastANI
[2024-01-24 12:37:30,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a519931-0149-4f4d-bccf-2fdb653a2d55/GCF_019684455.1_ASM1968445v1_genomic.fna.gz --refList GCF_019684455.1_ASM1968445v1_genomic.fna/target_genomes.txt --output GCF_019684455.1_ASM1968445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:50,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:50,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:50,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:50,023] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:50,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:50,023] [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 binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	100.0	2346	2348	95	conclusive
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	99.9952	2340	2348	95	conclusive
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	92.0792	1673	2348	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	91.4472	1618	2348	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	90.9801	1631	2348	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	88.7638	1651	2348	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	88.3567	1592	2348	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	88.1098	1633	2348	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	87.849	1590	2348	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.0936	1138	2348	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.3075	969	2348	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.9666	728	2348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:50,025] [INFO] DFAST Taxonomy check result was written to GCF_019684455.1_ASM1968445v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:50,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:50,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:50,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/checkm_data
[2024-01-24 12:37:50,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:50,091] [INFO] Task started: CheckM
[2024-01-24 12:37:50,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019684455.1_ASM1968445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019684455.1_ASM1968445v1_genomic.fna/checkm_input GCF_019684455.1_ASM1968445v1_genomic.fna/checkm_result
[2024-01-24 12:38:48,166] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:48,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:48,191] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:48,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:48,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019684455.1_ASM1968445v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:48,192] [INFO] Task started: Blastn
[2024-01-24 12:38:48,193] [INFO] Running command: blastn -query GCF_019684455.1_ASM1968445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b76e59d-f756-40a8-9b31-33880869422a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019684455.1_ASM1968445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:50,160] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:50,164] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:50,165] [INFO] Target genome list was writen to GCF_019684455.1_ASM1968445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:50,181] [INFO] Task started: fastANI
[2024-01-24 12:38:50,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a519931-0149-4f4d-bccf-2fdb653a2d55/GCF_019684455.1_ASM1968445v1_genomic.fna.gz --refList GCF_019684455.1_ASM1968445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019684455.1_ASM1968445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:08,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:08,952] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:08,953] [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_017357225.1	s__Rhizobium binae	99.9952	2341	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003985125.1	s__Rhizobium phaseoli	92.0869	1672	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_002531955.1	s__Rhizobium sp002531955	91.4897	1669	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_003939025.1	s__Rhizobium sophoriradicis	90.9988	1629	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	90.8995	1662	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200175.1	s__Rhizobium lentis_A	90.8487	1629	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCF_000092045.1	s__Rhizobium etli	88.757	1654	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	-
GCF_001664485.1	s__Rhizobium sp001664485	88.4582	1647	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_001187535.1	s__Rhizobium ecuadorense	88.3753	1589	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.31	0.89	0.89	4	-
GCF_000172795.2	s__Rhizobium sp000172795	88.2257	1571	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094625.1	s__Rhizobium aethiopicum	87.849	1590	2348	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:08,954] [INFO] GTDB search result was written to GCF_019684455.1_ASM1968445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:08,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:08,958] [INFO] DFAST_QC result json was written to GCF_019684455.1_ASM1968445v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:08,958] [INFO] DFAST_QC completed!
[2024-01-24 12:39:08,958] [INFO] Total running time: 0h2m2s