[2024-01-25 20:04:35,946] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:35,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:35,948] [INFO] DQC Reference Directory: /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference
[2024-01-25 20:04:37,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:37,075] [INFO] Task started: Prodigal
[2024-01-25 20:04:37,075] [INFO] Running command: gunzip -c /var/lib/cwl/stg05099171-22ae-43c8-8ab8-3f3c8a36c854/GCF_002278135.2_ASM227813v2_genomic.fna.gz | prodigal -d GCF_002278135.2_ASM227813v2_genomic.fna/cds.fna -a GCF_002278135.2_ASM227813v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:02,296] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:02,297] [INFO] Task started: HMMsearch
[2024-01-25 20:05:02,297] [INFO] Running command: hmmsearch --tblout GCF_002278135.2_ASM227813v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/reference_markers.hmm GCF_002278135.2_ASM227813v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:02,597] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:02,598] [INFO] Found 6/6 markers.
[2024-01-25 20:05:02,662] [INFO] Query marker FASTA was written to GCF_002278135.2_ASM227813v2_genomic.fna/markers.fasta
[2024-01-25 20:05:02,662] [INFO] Task started: Blastn
[2024-01-25 20:05:02,662] [INFO] Running command: blastn -query GCF_002278135.2_ASM227813v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/reference_markers.fasta -out GCF_002278135.2_ASM227813v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:03,708] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:03,710] [INFO] Selected 17 target genomes.
[2024-01-25 20:05:03,710] [INFO] Target genome list was writen to GCF_002278135.2_ASM227813v2_genomic.fna/target_genomes.txt
[2024-01-25 20:05:03,712] [INFO] Task started: fastANI
[2024-01-25 20:05:03,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg05099171-22ae-43c8-8ab8-3f3c8a36c854/GCF_002278135.2_ASM227813v2_genomic.fna.gz --refList GCF_002278135.2_ASM227813v2_genomic.fna/target_genomes.txt --output GCF_002278135.2_ASM227813v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:43,826] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:43,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:43,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:43,838] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:43,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:43,838] [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
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	100.0	2865	2868	95	conclusive
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	94.797	2308	2868	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	91.9831	1959	2868	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	91.7395	1990	2868	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	90.7064	2027	2868	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000284375.1	375	375	type	True	90.2892	2196	2868	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	90.1592	2087	2868	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	90.1466	2130	2868	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	90.1064	2175	2868	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	90.0521	2108	2868	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	89.1673	1971	2868	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	89.1396	2115	2868	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	89.1185	2018	2868	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	88.7933	1816	2868	95	below_threshold
Bradyrhizobium vignae	strain=LMG 28791	GCA_004114425.1	1549949	1549949	type	True	88.7715	1927	2868	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.9616	1516	2868	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.6971	1445	2868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:43,839] [INFO] DFAST Taxonomy check result was written to GCF_002278135.2_ASM227813v2_genomic.fna/tc_result.tsv
[2024-01-25 20:05:43,840] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:43,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:43,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/checkm_data
[2024-01-25 20:05:43,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:43,928] [INFO] Task started: CheckM
[2024-01-25 20:05:43,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002278135.2_ASM227813v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002278135.2_ASM227813v2_genomic.fna/checkm_input GCF_002278135.2_ASM227813v2_genomic.fna/checkm_result
[2024-01-25 20:07:09,781] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:09,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:09,802] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:09,802] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:09,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002278135.2_ASM227813v2_genomic.fna/markers.fasta)
[2024-01-25 20:07:09,803] [INFO] Task started: Blastn
[2024-01-25 20:07:09,803] [INFO] Running command: blastn -query GCF_002278135.2_ASM227813v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga7fa6d71-f9d8-49d1-b3aa-8c5673d1b0aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_002278135.2_ASM227813v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:12,015] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:12,018] [INFO] Selected 13 target genomes.
[2024-01-25 20:07:12,018] [INFO] Target genome list was writen to GCF_002278135.2_ASM227813v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:12,029] [INFO] Task started: fastANI
[2024-01-25 20:07:12,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg05099171-22ae-43c8-8ab8-3f3c8a36c854/GCF_002278135.2_ASM227813v2_genomic.fna.gz --refList GCF_002278135.2_ASM227813v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002278135.2_ASM227813v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:44,499] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:44,508] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:44,508] [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_002278135.2	s__Bradyrhizobium ottawaense	100.0	2865	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	conclusive
GCF_900094605.1	s__Bradyrhizobium shewense	94.7945	2308	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.95	97.95	0.88	0.88	2	-
GCF_900114915.1	s__Bradyrhizobium sp900114915	94.4418	2271	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.76	97.31	0.89	0.88	8	-
GCF_002266465.2	s__Bradyrhizobium symbiodeficiens	91.9831	1959	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.63	98.60	0.94	0.93	4	-
GCF_002266435.2	s__Bradyrhizobium amphicarpaeae	91.7323	1992	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776695.1	s__Bradyrhizobium nitroreducens	90.7145	2026	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.68	98.68	0.93	0.93	2	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	90.5397	2071	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284375.1	s__Bradyrhizobium japonicum	90.2832	2198	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.38	95.55	0.91	0.80	22	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	90.0747	1865	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963435.1	s__Bradyrhizobium sp003963435	90.0167	1485	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130245.1	s__Bradyrhizobium japonicum_F	89.849	1928	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016031635.1	s__Bradyrhizobium diversitatis	89.1556	1973	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.2113	96.64	96.14	0.84	0.83	6	-
GCF_011516635.3	s__Bradyrhizobium sp011516635	88.7521	2064	2868	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	96.65	95.57	0.79	0.75	11	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:44,510] [INFO] GTDB search result was written to GCF_002278135.2_ASM227813v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:44,510] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:44,513] [INFO] DFAST_QC result json was written to GCF_002278135.2_ASM227813v2_genomic.fna/dqc_result.json
[2024-01-25 20:07:44,513] [INFO] DFAST_QC completed!
[2024-01-25 20:07:44,513] [INFO] Total running time: 0h3m9s