[2023-06-05 04:42:59,234] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:42:59,238] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:42:59,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference
[2023-06-05 04:43:01,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:43:01,511] [INFO] Task started: Prodigal
[2023-06-05 04:43:01,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg65c4975d-4e89-4efa-828e-aeeb8cb3592a/GCA_004963545.1_ASM496354v1_genomic.fna.gz | prodigal -d GCA_004963545.1_ASM496354v1_genomic.fna/cds.fna -a GCA_004963545.1_ASM496354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:43:18,367] [INFO] Task succeeded: Prodigal
[2023-06-05 04:43:18,367] [INFO] Task started: HMMsearch
[2023-06-05 04:43:18,367] [INFO] Running command: hmmsearch --tblout GCA_004963545.1_ASM496354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/reference_markers.hmm GCA_004963545.1_ASM496354v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:43:18,670] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:43:18,672] [INFO] Found 6/6 markers.
[2023-06-05 04:43:18,726] [INFO] Query marker FASTA was written to GCA_004963545.1_ASM496354v1_genomic.fna/markers.fasta
[2023-06-05 04:43:18,726] [INFO] Task started: Blastn
[2023-06-05 04:43:18,726] [INFO] Running command: blastn -query GCA_004963545.1_ASM496354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/reference_markers.fasta -out GCA_004963545.1_ASM496354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:43:19,721] [INFO] Task succeeded: Blastn
[2023-06-05 04:43:19,726] [INFO] Selected 14 target genomes.
[2023-06-05 04:43:19,726] [INFO] Target genome list was writen to GCA_004963545.1_ASM496354v1_genomic.fna/target_genomes.txt
[2023-06-05 04:43:19,728] [INFO] Task started: fastANI
[2023-06-05 04:43:19,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c4975d-4e89-4efa-828e-aeeb8cb3592a/GCA_004963545.1_ASM496354v1_genomic.fna.gz --refList GCA_004963545.1_ASM496354v1_genomic.fna/target_genomes.txt --output GCA_004963545.1_ASM496354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:43:39,610] [INFO] Task succeeded: fastANI
[2023-06-05 04:43:39,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:43:39,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:43:39,627] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:43:39,627] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:43:39,627] [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
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	89.547	1368	1906	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	89.1966	1446	1906	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	86.987	1382	1906	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	86.7095	1367	1906	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	84.5935	1314	1906	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.4709	1168	1906	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	84.378	1292	1906	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.2563	1328	1906	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.0453	1168	1906	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	83.8826	1268	1906	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.6734	1221	1906	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0373	583	1906	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9129	568	1906	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.5225	491	1906	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:43:39,629] [INFO] DFAST Taxonomy check result was written to GCA_004963545.1_ASM496354v1_genomic.fna/tc_result.tsv
[2023-06-05 04:43:39,630] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:43:39,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:43:39,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/checkm_data
[2023-06-05 04:43:39,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:43:39,692] [INFO] Task started: CheckM
[2023-06-05 04:43:39,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004963545.1_ASM496354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004963545.1_ASM496354v1_genomic.fna/checkm_input GCA_004963545.1_ASM496354v1_genomic.fna/checkm_result
[2023-06-05 04:44:28,599] [INFO] Task succeeded: CheckM
[2023-06-05 04:44:28,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 04:44:28,626] [INFO] ===== Completeness check finished =====
[2023-06-05 04:44:28,626] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:44:28,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004963545.1_ASM496354v1_genomic.fna/markers.fasta)
[2023-06-05 04:44:28,627] [INFO] Task started: Blastn
[2023-06-05 04:44:28,627] [INFO] Running command: blastn -query GCA_004963545.1_ASM496354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76bdcdf8-0e8e-4c9a-a6f2-3b507e4e0d0a/dqc_reference/reference_markers_gtdb.fasta -out GCA_004963545.1_ASM496354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:44:30,604] [INFO] Task succeeded: Blastn
[2023-06-05 04:44:30,609] [INFO] Selected 12 target genomes.
[2023-06-05 04:44:30,610] [INFO] Target genome list was writen to GCA_004963545.1_ASM496354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:44:30,611] [INFO] Task started: fastANI
[2023-06-05 04:44:30,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c4975d-4e89-4efa-828e-aeeb8cb3592a/GCA_004963545.1_ASM496354v1_genomic.fna.gz --refList GCA_004963545.1_ASM496354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004963545.1_ASM496354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:44:49,887] [INFO] Task succeeded: fastANI
[2023-06-05 04:44:49,912] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:44:49,912] [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_002294985.1	s__Mesorhizobium sp002294985	97.183	1649	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.32	96.92	0.87	0.76	62	conclusive
GCF_002294995.1	s__Mesorhizobium sp002294995	94.1482	1601	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	90.0682	1485	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCA_004963905.1	s__Mesorhizobium sp004963905	89.9959	1479	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952465.1	s__Mesorhizobium sp003952465	89.6435	1532	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCA_004020545.1	s__Mesorhizobium sp004020545	89.629	1426	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_014843825.1	s__Mesorhizobium silamurunense	89.5371	1369	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_003952485.1	s__Mesorhizobium sp003952485	89.5099	1502	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCF_004791585.1	s__Mesorhizobium sp004791585	89.4306	1465	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003863365.1	s__Mesorhizobium tamadayense	89.206	1445	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510895.1	s__Mesorhizobium loti_A	89.1301	1418	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824825.2	s__Mesorhizobium sp000824825	88.7138	1407	1906	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:44:49,917] [INFO] GTDB search result was written to GCA_004963545.1_ASM496354v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:44:49,918] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:44:49,922] [INFO] DFAST_QC result json was written to GCA_004963545.1_ASM496354v1_genomic.fna/dqc_result.json
[2023-06-05 04:44:49,923] [INFO] DFAST_QC completed!
[2023-06-05 04:44:49,923] [INFO] Total running time: 0h1m51s