[2024-01-25 18:15:35,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference
[2024-01-25 18:15:36,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,655] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d128153-d35f-4b78-990c-bb27cca53ef5/GCF_031453995.1_ASM3145399v1_genomic.fna.gz | prodigal -d GCF_031453995.1_ASM3145399v1_genomic.fna/cds.fna -a GCF_031453995.1_ASM3145399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:47,621] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:47,621] [INFO] Task started: HMMsearch
[2024-01-25 18:15:47,621] [INFO] Running command: hmmsearch --tblout GCF_031453995.1_ASM3145399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/reference_markers.hmm GCF_031453995.1_ASM3145399v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:47,854] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:47,855] [INFO] Found 6/6 markers.
[2024-01-25 18:15:47,897] [INFO] Query marker FASTA was written to GCF_031453995.1_ASM3145399v1_genomic.fna/markers.fasta
[2024-01-25 18:15:47,897] [INFO] Task started: Blastn
[2024-01-25 18:15:47,897] [INFO] Running command: blastn -query GCF_031453995.1_ASM3145399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/reference_markers.fasta -out GCF_031453995.1_ASM3145399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:48,803] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:48,819] [INFO] Selected 19 target genomes.
[2024-01-25 18:15:48,819] [INFO] Target genome list was writen to GCF_031453995.1_ASM3145399v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:48,834] [INFO] Task started: fastANI
[2024-01-25 18:15:48,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d128153-d35f-4b78-990c-bb27cca53ef5/GCF_031453995.1_ASM3145399v1_genomic.fna.gz --refList GCF_031453995.1_ASM3145399v1_genomic.fna/target_genomes.txt --output GCF_031453995.1_ASM3145399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:12,848] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:12,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:12,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:12,860] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:16:12,860] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:16:12,860] [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
Nitrobacter winogradskyi	strain=Nb-255	GCA_000012725.1	913	913	type	True	86.5926	857	1379	95	below_threshold
Nitrobacter hamburgensis	strain=X14	GCA_000013885.1	912	912	type	True	84.8711	908	1379	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	79.1554	493	1379	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	78.9176	505	1379	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	78.8573	492	1379	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	78.8551	450	1379	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	78.7874	493	1379	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	78.7805	452	1379	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	78.7773	482	1379	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	78.7517	460	1379	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	78.728	449	1379	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	78.7143	503	1379	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	78.7024	470	1379	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	78.6843	493	1379	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	78.6341	439	1379	95	below_threshold
Bradyrhizobium cytisi	strain=CTAW11	GCA_008123515.1	515489	515489	type	True	78.6328	434	1379	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	78.6298	462	1379	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	78.4575	464	1379	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	78.4566	450	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:12,862] [INFO] DFAST Taxonomy check result was written to GCF_031453995.1_ASM3145399v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:12,862] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:12,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:12,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/checkm_data
[2024-01-25 18:16:12,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:12,906] [INFO] Task started: CheckM
[2024-01-25 18:16:12,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031453995.1_ASM3145399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031453995.1_ASM3145399v1_genomic.fna/checkm_input GCF_031453995.1_ASM3145399v1_genomic.fna/checkm_result
[2024-01-25 18:16:46,986] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:46,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:47,002] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:47,002] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:47,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031453995.1_ASM3145399v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:47,003] [INFO] Task started: Blastn
[2024-01-25 18:16:47,003] [INFO] Running command: blastn -query GCF_031453995.1_ASM3145399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe084354-906e-4b5e-a5bb-517aec034751/dqc_reference/reference_markers_gtdb.fasta -out GCF_031453995.1_ASM3145399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:48,832] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:48,835] [INFO] Selected 7 target genomes.
[2024-01-25 18:16:48,835] [INFO] Target genome list was writen to GCF_031453995.1_ASM3145399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:48,847] [INFO] Task started: fastANI
[2024-01-25 18:16:48,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d128153-d35f-4b78-990c-bb27cca53ef5/GCF_031453995.1_ASM3145399v1_genomic.fna.gz --refList GCF_031453995.1_ASM3145399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031453995.1_ASM3145399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:55,747] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:55,756] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:55,757] [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_002028545.1	s__Nitrobacter vulgaris	98.2895	1080	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000152905.1	s__Nitrobacter sp000152905	88.1889	965	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539545.1	s__Nitrobacter winogradskyi_A	86.7868	856	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012725.1	s__Nitrobacter winogradskyi	86.5947	857	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013885.1	s__Nitrobacter hamburgensis	84.8669	906	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897285.1	s__Nitrobacter sp001897285	83.1	751	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_001896955.1	s__Nitrobacter sp001896955	83.0424	713	1379	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:55,758] [INFO] GTDB search result was written to GCF_031453995.1_ASM3145399v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:55,760] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:55,763] [INFO] DFAST_QC result json was written to GCF_031453995.1_ASM3145399v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:55,763] [INFO] DFAST_QC completed!
[2024-01-25 18:16:55,763] [INFO] Total running time: 0h1m20s