[2024-01-24 11:21:07,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,408] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference
[2024-01-24 11:21:11,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,964] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg62b6b4ff-064f-453b-b03d-dbe8c2158b9d/GCF_013114835.1_ASM1311483v1_genomic.fna.gz | prodigal -d GCF_013114835.1_ASM1311483v1_genomic.fna/cds.fna -a GCF_013114835.1_ASM1311483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:32,900] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:32,901] [INFO] Task started: HMMsearch
[2024-01-24 11:21:32,901] [INFO] Running command: hmmsearch --tblout GCF_013114835.1_ASM1311483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/reference_markers.hmm GCF_013114835.1_ASM1311483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:33,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:33,236] [INFO] Found 6/6 markers.
[2024-01-24 11:21:33,290] [INFO] Query marker FASTA was written to GCF_013114835.1_ASM1311483v1_genomic.fna/markers.fasta
[2024-01-24 11:21:33,290] [INFO] Task started: Blastn
[2024-01-24 11:21:33,290] [INFO] Running command: blastn -query GCF_013114835.1_ASM1311483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/reference_markers.fasta -out GCF_013114835.1_ASM1311483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:34,294] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:34,297] [INFO] Selected 18 target genomes.
[2024-01-24 11:21:34,297] [INFO] Target genome list was writen to GCF_013114835.1_ASM1311483v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:34,306] [INFO] Task started: fastANI
[2024-01-24 11:21:34,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b6b4ff-064f-453b-b03d-dbe8c2158b9d/GCF_013114835.1_ASM1311483v1_genomic.fna.gz --refList GCF_013114835.1_ASM1311483v1_genomic.fna/target_genomes.txt --output GCF_013114835.1_ASM1311483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:22:09,356] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:09,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:22:09,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:22:09,382] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:22:09,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:22:09,382] [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 archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	100.0	2319	2322	95	conclusive
Bradyrhizobium australiense	strain=WSM 1791	GCA_013114825.1	2721161	2721161	type	True	88.724	1914	2322	95	below_threshold
Bradyrhizobium murdochi	strain=WSM 1741	GCA_000472965.1	1038859	1038859	type	True	88.6591	1911	2322	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	88.2828	1868	2322	95	below_threshold
Bradyrhizobium retamae	strain=Ro19	GCA_001440415.1	1300035	1300035	type	True	88.0536	1835	2322	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	87.9406	1854	2322	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	87.9032	1775	2322	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	87.8938	1840	2322	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	87.357	1738	2322	95	below_threshold
Bradyrhizobium mercantei	strain=SEMIA 6399	GCA_001982635.1	1904807	1904807	type	True	82.9132	1339	2322	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	82.9116	1443	2322	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	82.8229	1428	2322	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	82.7949	1421	2322	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	82.7909	1397	2322	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	82.7588	1379	2322	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	82.5946	1293	2322	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	82.5833	1389	2322	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	82.5763	1308	2322	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:22:09,384] [INFO] DFAST Taxonomy check result was written to GCF_013114835.1_ASM1311483v1_genomic.fna/tc_result.tsv
[2024-01-24 11:22:09,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:22:09,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:22:09,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/checkm_data
[2024-01-24 11:22:09,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:22:09,450] [INFO] Task started: CheckM
[2024-01-24 11:22:09,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013114835.1_ASM1311483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013114835.1_ASM1311483v1_genomic.fna/checkm_input GCF_013114835.1_ASM1311483v1_genomic.fna/checkm_result
[2024-01-24 11:23:06,930] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:06,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:06,948] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:06,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:06,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013114835.1_ASM1311483v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:06,949] [INFO] Task started: Blastn
[2024-01-24 11:23:06,949] [INFO] Running command: blastn -query GCF_013114835.1_ASM1311483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaacd645-aafc-438f-9866-b1399a54f287/dqc_reference/reference_markers_gtdb.fasta -out GCF_013114835.1_ASM1311483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:09,035] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:09,039] [INFO] Selected 17 target genomes.
[2024-01-24 11:23:09,039] [INFO] Target genome list was writen to GCF_013114835.1_ASM1311483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:09,050] [INFO] Task started: fastANI
[2024-01-24 11:23:09,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg62b6b4ff-064f-453b-b03d-dbe8c2158b9d/GCF_013114835.1_ASM1311483v1_genomic.fna.gz --refList GCF_013114835.1_ASM1311483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013114835.1_ASM1311483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:41,456] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:41,471] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:41,471] [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_013114835.1	s__Bradyrhizobium archetypum	100.0	2319	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013114825.1	s__Bradyrhizobium australiense	88.7028	1918	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693485.1	s__Bradyrhizobium sp001693485	88.6706	1902	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472965.1	s__Bradyrhizobium murdochi	88.6587	1910	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693385.1	s__Bradyrhizobium icense	88.2844	1868	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440415.1	s__Bradyrhizobium retamae	88.0612	1834	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398875.1	s__Bradyrhizobium sp018398875	88.034	1845	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693515.2	s__Bradyrhizobium paxllaeri	87.9297	1857	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440405.1	s__Bradyrhizobium valentinum	87.9142	1774	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.35	99.35	0.91	0.91	2	-
GCF_018398895.1	s__Bradyrhizobium sp018398895	87.913	1867	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440475.1	s__Bradyrhizobium lablabi	87.8987	1839	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130385.1	s__Bradyrhizobium sp018130385	87.6405	1677	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440395.1	s__Bradyrhizobium jicamae	87.3414	1741	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018130505.1	s__Bradyrhizobium tropiciagri_B	82.9638	1347	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900696085.1	s__Bradyrhizobium ivorense	82.9017	1446	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.20	96.86	0.90	0.88	3	-
GCF_015624485.1	s__Bradyrhizobium sp015624485	82.7772	1325	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018131005.1	s__Bradyrhizobium lablabi_D	81.8297	1247	2322	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:41,472] [INFO] GTDB search result was written to GCF_013114835.1_ASM1311483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:41,473] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:41,476] [INFO] DFAST_QC result json was written to GCF_013114835.1_ASM1311483v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:41,477] [INFO] DFAST_QC completed!
[2024-01-24 11:23:41,477] [INFO] Total running time: 0h2m34s