[2023-06-04 18:00:15,752] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:15,756] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:15,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference
[2023-06-04 18:00:16,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:16,985] [INFO] Task started: Prodigal
[2023-06-04 18:00:16,985] [INFO] Running command: gunzip -c /var/lib/cwl/stg24b608ec-598b-4892-b57b-1a5c3a317501/GCA_004016595.1_ASM401659v1_genomic.fna.gz | prodigal -d GCA_004016595.1_ASM401659v1_genomic.fna/cds.fna -a GCA_004016595.1_ASM401659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:38,081] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:38,081] [INFO] Task started: HMMsearch
[2023-06-04 18:00:38,081] [INFO] Running command: hmmsearch --tblout GCA_004016595.1_ASM401659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/reference_markers.hmm GCA_004016595.1_ASM401659v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:38,460] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:38,463] [INFO] Found 6/6 markers.
[2023-06-04 18:00:38,522] [INFO] Query marker FASTA was written to GCA_004016595.1_ASM401659v1_genomic.fna/markers.fasta
[2023-06-04 18:00:38,522] [INFO] Task started: Blastn
[2023-06-04 18:00:38,522] [INFO] Running command: blastn -query GCA_004016595.1_ASM401659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/reference_markers.fasta -out GCA_004016595.1_ASM401659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:39,642] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:39,646] [INFO] Selected 13 target genomes.
[2023-06-04 18:00:39,646] [INFO] Target genome list was writen to GCA_004016595.1_ASM401659v1_genomic.fna/target_genomes.txt
[2023-06-04 18:00:39,648] [INFO] Task started: fastANI
[2023-06-04 18:00:39,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b608ec-598b-4892-b57b-1a5c3a317501/GCA_004016595.1_ASM401659v1_genomic.fna.gz --refList GCA_004016595.1_ASM401659v1_genomic.fna/target_genomes.txt --output GCA_004016595.1_ASM401659v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:01:02,019] [INFO] Task succeeded: fastANI
[2023-06-04 18:01:02,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:01:02,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:01:02,034] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:01:02,034] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:01:02,034] [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	90.1812	1604	2330	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	89.8741	1742	2330	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	87.4716	1663	2330	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	87.4025	1605	2330	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	85.4379	1596	2330	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	84.9759	1343	2330	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	84.6838	1549	2330	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	84.4851	1374	2330	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	84.0518	1400	2330	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	84.0015	1376	2330	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.9936	660	2330	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.9729	694	2330	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.7505	538	2330	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:01:02,036] [INFO] DFAST Taxonomy check result was written to GCA_004016595.1_ASM401659v1_genomic.fna/tc_result.tsv
[2023-06-04 18:01:02,037] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:01:02,037] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:01:02,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/checkm_data
[2023-06-04 18:01:02,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:01:02,106] [INFO] Task started: CheckM
[2023-06-04 18:01:02,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004016595.1_ASM401659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004016595.1_ASM401659v1_genomic.fna/checkm_input GCA_004016595.1_ASM401659v1_genomic.fna/checkm_result
[2023-06-04 18:02:01,078] [INFO] Task succeeded: CheckM
[2023-06-04 18:02:01,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:02:01,106] [INFO] ===== Completeness check finished =====
[2023-06-04 18:02:01,107] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:02:01,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004016595.1_ASM401659v1_genomic.fna/markers.fasta)
[2023-06-04 18:02:01,107] [INFO] Task started: Blastn
[2023-06-04 18:02:01,107] [INFO] Running command: blastn -query GCA_004016595.1_ASM401659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95944c37-bad0-439b-8418-3579f8717998/dqc_reference/reference_markers_gtdb.fasta -out GCA_004016595.1_ASM401659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:02:03,334] [INFO] Task succeeded: Blastn
[2023-06-04 18:02:03,343] [INFO] Selected 13 target genomes.
[2023-06-04 18:02:03,343] [INFO] Target genome list was writen to GCA_004016595.1_ASM401659v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:02:03,344] [INFO] Task started: fastANI
[2023-06-04 18:02:03,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b608ec-598b-4892-b57b-1a5c3a317501/GCA_004016595.1_ASM401659v1_genomic.fna.gz --refList GCA_004016595.1_ASM401659v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004016595.1_ASM401659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:02:31,198] [INFO] Task succeeded: fastANI
[2023-06-04 18:02:31,213] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:02:31,213] [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_003952465.1	s__Mesorhizobium sp003952465	98.089	2150	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	conclusive
GCA_001510895.1	s__Mesorhizobium loti_A	91.6641	1747	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791585.1	s__Mesorhizobium sp004791585	90.8909	1798	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952385.1	s__Mesorhizobium sp003952385	90.8724	1798	2330	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	90.7489	1798	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	90.7135	1831	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_004020545.1	s__Mesorhizobium sp004020545	90.6664	1777	2330	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	90.1616	1606	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCA_000824825.2	s__Mesorhizobium sp000824825	89.467	1701	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002294995.1	s__Mesorhizobium sp002294995	89.3143	1629	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016445.2	s__Mesorhizobium sp004016445	88.1763	1721	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	96.92	0.94	0.90	3	-
GCF_019091085.1	s__Mesorhizobium sp019091085	87.9841	1551	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	86.6103	1619	2330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:02:31,216] [INFO] GTDB search result was written to GCA_004016595.1_ASM401659v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:02:31,217] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:02:31,220] [INFO] DFAST_QC result json was written to GCA_004016595.1_ASM401659v1_genomic.fna/dqc_result.json
[2023-06-04 18:02:31,220] [INFO] DFAST_QC completed!
[2023-06-04 18:02:31,221] [INFO] Total running time: 0h2m15s