[2024-01-24 14:20:01,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:01,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:01,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference
[2024-01-24 14:20:02,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,739] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,739] [INFO] Running command: gunzip -c /var/lib/cwl/stged84dc17-85a5-4630-a82f-d6d1469a89ad/GCF_014196505.1_ASM1419650v1_genomic.fna.gz | prodigal -d GCF_014196505.1_ASM1419650v1_genomic.fna/cds.fna -a GCF_014196505.1_ASM1419650v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:17,549] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:17,549] [INFO] Task started: HMMsearch
[2024-01-24 14:20:17,549] [INFO] Running command: hmmsearch --tblout GCF_014196505.1_ASM1419650v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/reference_markers.hmm GCF_014196505.1_ASM1419650v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:17,843] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:17,845] [INFO] Found 6/6 markers.
[2024-01-24 14:20:17,913] [INFO] Query marker FASTA was written to GCF_014196505.1_ASM1419650v1_genomic.fna/markers.fasta
[2024-01-24 14:20:17,913] [INFO] Task started: Blastn
[2024-01-24 14:20:17,913] [INFO] Running command: blastn -query GCF_014196505.1_ASM1419650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/reference_markers.fasta -out GCF_014196505.1_ASM1419650v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,957] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,961] [INFO] Selected 20 target genomes.
[2024-01-24 14:20:18,961] [INFO] Target genome list was writen to GCF_014196505.1_ASM1419650v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:19,036] [INFO] Task started: fastANI
[2024-01-24 14:20:19,036] [INFO] Running command: fastANI --query /var/lib/cwl/stged84dc17-85a5-4630-a82f-d6d1469a89ad/GCF_014196505.1_ASM1419650v1_genomic.fna.gz --refList GCF_014196505.1_ASM1419650v1_genomic.fna/target_genomes.txt --output GCF_014196505.1_ASM1419650v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:44,059] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:44,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:44,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:44,078] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:44,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:44,078] [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 metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	100.0	1687	1693	95	conclusive
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	82.4636	1006	1693	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	82.2968	1010	1693	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	82.2744	989	1693	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	82.264	992	1693	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	82.2631	947	1693	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	82.2339	986	1693	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	82.2302	1018	1693	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	82.2028	963	1693	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	82.1833	964	1693	95	below_threshold
Rhizobium altiplani	strain=BR 10423	GCA_001542405.1	1864509	1864509	type	True	82.1771	957	1693	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	82.165	993	1693	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	82.1495	990	1693	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	82.0882	1004	1693	95	below_threshold
Rhizobium tibeticum	strain=CGMCC 1.7071	GCA_900110205.1	501024	501024	type	True	82.0393	991	1693	95	below_threshold
Rhizobium tibeticum		GCA_900108425.1	501024	501024	type	True	82.0216	990	1693	95	below_threshold
Rhizobium favelukesii	strain=LPU83	GCA_000577275.2	348824	348824	type	True	81.9494	979	1693	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	80.963	930	1693	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.4471	711	1693	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3663	720	1693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:44,080] [INFO] DFAST Taxonomy check result was written to GCF_014196505.1_ASM1419650v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:44,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:44,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:44,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/checkm_data
[2024-01-24 14:20:44,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:44,139] [INFO] Task started: CheckM
[2024-01-24 14:20:44,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196505.1_ASM1419650v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196505.1_ASM1419650v1_genomic.fna/checkm_input GCF_014196505.1_ASM1419650v1_genomic.fna/checkm_result
[2024-01-24 14:21:28,273] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:28,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:28,294] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:28,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:28,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196505.1_ASM1419650v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:28,295] [INFO] Task started: Blastn
[2024-01-24 14:21:28,295] [INFO] Running command: blastn -query GCF_014196505.1_ASM1419650v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea650ce8-7e0a-46a5-add3-59ce007e0821/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196505.1_ASM1419650v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:30,378] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:30,382] [INFO] Selected 7 target genomes.
[2024-01-24 14:21:30,382] [INFO] Target genome list was writen to GCF_014196505.1_ASM1419650v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:30,403] [INFO] Task started: fastANI
[2024-01-24 14:21:30,403] [INFO] Running command: fastANI --query /var/lib/cwl/stged84dc17-85a5-4630-a82f-d6d1469a89ad/GCF_014196505.1_ASM1419650v1_genomic.fna.gz --refList GCF_014196505.1_ASM1419650v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196505.1_ASM1419650v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:41,157] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:41,169] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:41,169] [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_014196505.1	s__Rhizobium metallidurans	100.0	1687	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017741815.1	s__Rhizobium sp017741815	91.3233	1358	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000377565.1	s__Rhizobium sp000377565	91.2883	1389	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799775.1	s__Rhizobium sp000799775	91.2636	1373	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.27	95.13	0.81	0.79	16	-
GCA_900465665.1	s__Rhizobium sp900465665	91.203	1297	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900467745.1	s__Rhizobium sp900467745	90.9933	1363	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.53	95.77	0.88	0.84	8	-
GCA_900472605.1	s__Rhizobium sp900472605	90.1458	1319	1693	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.47	95.34	0.81	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:41,171] [INFO] GTDB search result was written to GCF_014196505.1_ASM1419650v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:41,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:41,174] [INFO] DFAST_QC result json was written to GCF_014196505.1_ASM1419650v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:41,175] [INFO] DFAST_QC completed!
[2024-01-24 14:21:41,175] [INFO] Total running time: 0h1m40s