[2024-01-24 11:05:03,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference
[2024-01-24 11:05:05,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,813] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dfdbd63-70ea-4f3d-97db-dbcbe5b7d332/GCF_029030725.1_ASM2903072v1_genomic.fna.gz | prodigal -d GCF_029030725.1_ASM2903072v1_genomic.fna/cds.fna -a GCF_029030725.1_ASM2903072v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:14,751] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:14,752] [INFO] Task started: HMMsearch
[2024-01-24 11:05:14,752] [INFO] Running command: hmmsearch --tblout GCF_029030725.1_ASM2903072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/reference_markers.hmm GCF_029030725.1_ASM2903072v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:15,001] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:15,003] [INFO] Found 6/6 markers.
[2024-01-24 11:05:15,033] [INFO] Query marker FASTA was written to GCF_029030725.1_ASM2903072v1_genomic.fna/markers.fasta
[2024-01-24 11:05:15,033] [INFO] Task started: Blastn
[2024-01-24 11:05:15,033] [INFO] Running command: blastn -query GCF_029030725.1_ASM2903072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/reference_markers.fasta -out GCF_029030725.1_ASM2903072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,032] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,034] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:16,035] [INFO] Target genome list was writen to GCF_029030725.1_ASM2903072v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:16,040] [INFO] Task started: fastANI
[2024-01-24 11:05:16,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfdbd63-70ea-4f3d-97db-dbcbe5b7d332/GCF_029030725.1_ASM2903072v1_genomic.fna.gz --refList GCF_029030725.1_ASM2903072v1_genomic.fna/target_genomes.txt --output GCF_029030725.1_ASM2903072v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:34,513] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:34,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:34,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:34,524] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:34,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:34,525] [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
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	87.5075	894	1090	95	below_threshold
Afipia felis	strain=NCTC12499	GCA_900445155.1	1035	1035	type	True	87.5056	895	1090	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	84.7334	814	1090	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	84.6606	813	1090	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	80.9413	570	1090	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	80.5249	595	1090	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	80.2955	582	1090	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	80.2562	565	1090	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	80.2205	568	1090	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	80.1808	558	1090	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	80.0013	576	1090	95	below_threshold
Bradyrhizobium daqingense	strain=CGMCC 1.10947	GCA_007830205.1	993502	993502	type	True	79.9422	560	1090	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	79.8933	566	1090	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	79.8808	569	1090	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	79.6752	553	1090	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	79.5444	539	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:34,526] [INFO] DFAST Taxonomy check result was written to GCF_029030725.1_ASM2903072v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:34,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:34,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:34,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/checkm_data
[2024-01-24 11:05:34,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:34,565] [INFO] Task started: CheckM
[2024-01-24 11:05:34,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029030725.1_ASM2903072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029030725.1_ASM2903072v1_genomic.fna/checkm_input GCF_029030725.1_ASM2903072v1_genomic.fna/checkm_result
[2024-01-24 11:06:05,090] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:05,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:05,106] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:05,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:05,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029030725.1_ASM2903072v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:05,107] [INFO] Task started: Blastn
[2024-01-24 11:06:05,107] [INFO] Running command: blastn -query GCF_029030725.1_ASM2903072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge94de672-8895-4130-b140-f786e203e88e/dqc_reference/reference_markers_gtdb.fasta -out GCF_029030725.1_ASM2903072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:07,217] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:07,220] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:07,220] [INFO] Target genome list was writen to GCF_029030725.1_ASM2903072v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:07,228] [INFO] Task started: fastANI
[2024-01-24 11:06:07,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfdbd63-70ea-4f3d-97db-dbcbe5b7d332/GCF_029030725.1_ASM2903072v1_genomic.fna.gz --refList GCF_029030725.1_ASM2903072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029030725.1_ASM2903072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:18,703] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:18,711] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:18,712] [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_000178995.1	s__Afipia sp000178995	91.0691	941	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.46	98.22	0.89	0.84	3	-
GCF_000314735.2	s__Afipia felis	87.5075	894	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.60	95.79	0.96	0.87	4	-
GCF_000218565.1	s__Afipia carboxidovorans	84.7209	815	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.99	99.99	1.00	1.00	3	-
GCA_001897755.1	s__Afipia sp001897755	82.5142	726	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017305455.1	s__Afipia sp017305455	82.3003	666	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425835.1	s__Afipia sp001425835	81.0584	629	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308575.1	s__Afipia sp001897905	80.9979	621	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
GCA_003963145.1	s__Afipia sp003963145	80.9494	607	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497575.1	s__Afipia sp000497575	80.8408	590	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.26	97.37	0.94	0.78	8	-
GCF_000308295.2	s__Afipia birgiae	80.2942	581	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	98.96	98.31	0.86	0.83	3	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	80.2135	549	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305665.1	s__Nitrobacter sp017305665	79.9835	525	1090	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,713] [INFO] GTDB search result was written to GCF_029030725.1_ASM2903072v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:18,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:18,716] [INFO] DFAST_QC result json was written to GCF_029030725.1_ASM2903072v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:18,716] [INFO] DFAST_QC completed!
[2024-01-24 11:06:18,716] [INFO] Total running time: 0h1m15s