[2024-01-24 11:05:03,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,935] [INFO] DQC Reference Directory: /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg72ccefd4-843a-4bb9-9c30-71eede045102/GCF_008727715.1_ASM872771v1_genomic.fna.gz | prodigal -d GCF_008727715.1_ASM872771v1_genomic.fna/cds.fna -a GCF_008727715.1_ASM872771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:22,718] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:22,718] [INFO] Task started: HMMsearch
[2024-01-24 11:05:22,718] [INFO] Running command: hmmsearch --tblout GCF_008727715.1_ASM872771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/reference_markers.hmm GCF_008727715.1_ASM872771v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:23,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:23,052] [INFO] Found 6/6 markers.
[2024-01-24 11:05:23,096] [INFO] Query marker FASTA was written to GCF_008727715.1_ASM872771v1_genomic.fna/markers.fasta
[2024-01-24 11:05:23,096] [INFO] Task started: Blastn
[2024-01-24 11:05:23,096] [INFO] Running command: blastn -query GCF_008727715.1_ASM872771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/reference_markers.fasta -out GCF_008727715.1_ASM872771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:24,085] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:24,087] [INFO] Selected 30 target genomes.
[2024-01-24 11:05:24,088] [INFO] Target genome list was writen to GCF_008727715.1_ASM872771v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:24,108] [INFO] Task started: fastANI
[2024-01-24 11:05:24,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ccefd4-843a-4bb9-9c30-71eede045102/GCF_008727715.1_ASM872771v1_genomic.fna.gz --refList GCF_008727715.1_ASM872771v1_genomic.fna/target_genomes.txt --output GCF_008727715.1_ASM872771v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:05,530] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:05,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:05,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:05,547] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:05,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:05,548] [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 hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	81.8616	1069	2007	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	81.7899	1069	2007	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	81.7508	1032	2007	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	81.679	1052	2007	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	81.6671	1019	2007	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	81.6352	968	2007	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	81.6048	972	2007	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	81.5847	1039	2007	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	81.5812	1105	2007	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	81.5632	1055	2007	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	81.483	1087	2007	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	81.4551	1050	2007	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	81.4396	927	2007	95	below_threshold
Mesorhizobium loti	strain=DSM 2626	GCA_003148495.1	381	381	suspected-type	True	81.4196	1079	2007	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	81.3346	938	2007	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	81.261	890	2007	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	81.2308	954	2007	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	81.0568	859	2007	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	81.0162	934	2007	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	80.9543	953	2007	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	80.7062	916	2007	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	80.5097	888	2007	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	80.2537	671	2007	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	79.6298	705	2007	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	79.3545	660	2007	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	79.1037	650	2007	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	79.1006	651	2007	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	79.0298	612	2007	95	below_threshold
Phyllobacterium myrsinacearum	strain=DSM 5892	GCA_002980555.1	28101	28101	type	True	77.6655	468	2007	95	below_threshold
Phyllobacterium myrsinacearum	strain=IAM 13584	GCA_003182235.1	28101	28101	type	True	77.6472	463	2007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:05,549] [INFO] DFAST Taxonomy check result was written to GCF_008727715.1_ASM872771v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:05,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:05,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:05,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/checkm_data
[2024-01-24 11:06:05,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:05,605] [INFO] Task started: CheckM
[2024-01-24 11:06:05,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008727715.1_ASM872771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008727715.1_ASM872771v1_genomic.fna/checkm_input GCF_008727715.1_ASM872771v1_genomic.fna/checkm_result
[2024-01-24 11:06:55,161] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:55,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:55,177] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:55,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:55,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008727715.1_ASM872771v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:55,178] [INFO] Task started: Blastn
[2024-01-24 11:06:55,178] [INFO] Running command: blastn -query GCF_008727715.1_ASM872771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf930c35f-b74d-425b-b8c5-88e7c339d452/dqc_reference/reference_markers_gtdb.fasta -out GCF_008727715.1_ASM872771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:57,145] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:57,148] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:57,148] [INFO] Target genome list was writen to GCF_008727715.1_ASM872771v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:57,172] [INFO] Task started: fastANI
[2024-01-24 11:06:57,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ccefd4-843a-4bb9-9c30-71eede045102/GCF_008727715.1_ASM872771v1_genomic.fna.gz --refList GCF_008727715.1_ASM872771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008727715.1_ASM872771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:21,625] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:21,636] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:21,636] [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_008727715.1	s__Mesorhizobium terrae	100.0	2007	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.80	99.17	0.95	0.89	9	conclusive
GCF_001303895.1	s__Mesorhizobium sp001303895	84.1649	1338	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858745.1	s__Mesorhizobium loti_F	83.8289	1326	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004136315.1	s__Mesorhizobium sp004136315	83.8047	1356	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.54	97.14	0.95	0.93	3	-
GCF_004791585.1	s__Mesorhizobium sp004791585	81.8797	1031	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.07	98.11	0.95	0.89	24	-
GCF_003952465.1	s__Mesorhizobium sp003952465	81.8343	1059	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_014843825.1	s__Mesorhizobium silamurunense	81.6261	969	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	81.5967	1101	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854785.1	s__Mesorhizobium sp001854785	81.4591	1001	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830515.1	s__Mesorhizobium tianshanense	81.308	975	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472785.1	s__Mesorhizobium loti_E	81.3025	1060	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442685.1	s__Mesorhizobium sp006442685	81.2884	1021	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.73	95.49	0.95	0.85	44	-
GCF_014206975.1	s__Aminobacter aganoensis	81.2607	890	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_014200015.1	s__Aminobacter niigataensis	81.0886	854	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_000372965.1	s__Aminobacter sp000372965	80.8464	946	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724355.1	s__Aminobacter sp001724355	80.8341	666	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148805.1	s__Aminobacter sp003148805	80.5042	835	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012705.1	s__Pseudaminobacter soli	80.4515	876	2007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:21,637] [INFO] GTDB search result was written to GCF_008727715.1_ASM872771v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:21,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:21,642] [INFO] DFAST_QC result json was written to GCF_008727715.1_ASM872771v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:21,642] [INFO] DFAST_QC completed!
[2024-01-24 11:07:21,642] [INFO] Total running time: 0h2m18s