[2024-01-25 19:12:35,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:35,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:35,778] [INFO] DQC Reference Directory: /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference
[2024-01-25 19:12:36,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:36,910] [INFO] Task started: Prodigal
[2024-01-25 19:12:36,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1c1b646-cd03-4183-a11d-4a2b51255150/GCF_003985125.1_ASM398512v1_genomic.fna.gz | prodigal -d GCF_003985125.1_ASM398512v1_genomic.fna/cds.fna -a GCF_003985125.1_ASM398512v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:53,718] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:53,718] [INFO] Task started: HMMsearch
[2024-01-25 19:12:53,718] [INFO] Running command: hmmsearch --tblout GCF_003985125.1_ASM398512v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/reference_markers.hmm GCF_003985125.1_ASM398512v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:54,038] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:54,039] [INFO] Found 6/6 markers.
[2024-01-25 19:12:54,089] [INFO] Query marker FASTA was written to GCF_003985125.1_ASM398512v1_genomic.fna/markers.fasta
[2024-01-25 19:12:54,089] [INFO] Task started: Blastn
[2024-01-25 19:12:54,089] [INFO] Running command: blastn -query GCF_003985125.1_ASM398512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/reference_markers.fasta -out GCF_003985125.1_ASM398512v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:55,067] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:55,069] [INFO] Selected 13 target genomes.
[2024-01-25 19:12:55,070] [INFO] Target genome list was writen to GCF_003985125.1_ASM398512v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:55,071] [INFO] Task started: fastANI
[2024-01-25 19:12:55,071] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c1b646-cd03-4183-a11d-4a2b51255150/GCF_003985125.1_ASM398512v1_genomic.fna.gz --refList GCF_003985125.1_ASM398512v1_genomic.fna/target_genomes.txt --output GCF_003985125.1_ASM398512v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:15,448] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:15,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:15,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:15,457] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:13:15,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:13:15,457] [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 phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	100.0	2171	2178	95	conclusive
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	92.4516	1782	2178	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	92.2594	1825	2178	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	92.0631	1685	2178	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	92.0226	1694	2178	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	89.9941	1768	2178	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	89.7445	1674	2178	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	89.3103	1704	2178	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.1823	1728	2178	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	88.7276	1743	2178	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.1391	1161	2178	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.5888	976	2178	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.468	680	2178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:15,459] [INFO] DFAST Taxonomy check result was written to GCF_003985125.1_ASM398512v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:15,459] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:15,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:15,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/checkm_data
[2024-01-25 19:13:15,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:15,522] [INFO] Task started: CheckM
[2024-01-25 19:13:15,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003985125.1_ASM398512v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003985125.1_ASM398512v1_genomic.fna/checkm_input GCF_003985125.1_ASM398512v1_genomic.fna/checkm_result
[2024-01-25 19:14:03,068] [INFO] Task succeeded: CheckM
[2024-01-25 19:14:03,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:14:03,089] [INFO] ===== Completeness check finished =====
[2024-01-25 19:14:03,089] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:14:03,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003985125.1_ASM398512v1_genomic.fna/markers.fasta)
[2024-01-25 19:14:03,091] [INFO] Task started: Blastn
[2024-01-25 19:14:03,091] [INFO] Running command: blastn -query GCF_003985125.1_ASM398512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08c9e27-e621-4d84-b8e3-101dc43c5eff/dqc_reference/reference_markers_gtdb.fasta -out GCF_003985125.1_ASM398512v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:14:05,178] [INFO] Task succeeded: Blastn
[2024-01-25 19:14:05,186] [INFO] Selected 9 target genomes.
[2024-01-25 19:14:05,186] [INFO] Target genome list was writen to GCF_003985125.1_ASM398512v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:14:05,192] [INFO] Task started: fastANI
[2024-01-25 19:14:05,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c1b646-cd03-4183-a11d-4a2b51255150/GCF_003985125.1_ASM398512v1_genomic.fna.gz --refList GCF_003985125.1_ASM398512v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003985125.1_ASM398512v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:22,121] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:22,128] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:22,128] [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_003985125.1	s__Rhizobium phaseoli	100.0	2171	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	conclusive
GCF_002531955.1	s__Rhizobium sp002531955	92.6877	1820	2178	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	92.2514	1825	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_017357225.1	s__Rhizobium binae	92.0621	1685	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014200175.1	s__Rhizobium lentis_A	91.4843	1739	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	91.4287	1681	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092045.1	s__Rhizobium etli	90.0039	1765	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	-
GCF_002531825.1	s__Rhizobium sp002531825	89.3929	1690	2178	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	88.7254	1743	2178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:22,130] [INFO] GTDB search result was written to GCF_003985125.1_ASM398512v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:22,130] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:22,133] [INFO] DFAST_QC result json was written to GCF_003985125.1_ASM398512v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:22,134] [INFO] DFAST_QC completed!
[2024-01-25 19:14:22,134] [INFO] Total running time: 0h1m46s