[2024-01-24 12:34:20,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference
[2024-01-24 12:34:21,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,773] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d0b02da-66f5-4e99-b670-c0d6d4895bbe/GCF_003403035.1_ASM340303v1_genomic.fna.gz | prodigal -d GCF_003403035.1_ASM340303v1_genomic.fna/cds.fna -a GCF_003403035.1_ASM340303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:35,307] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:35,307] [INFO] Task started: HMMsearch
[2024-01-24 12:34:35,308] [INFO] Running command: hmmsearch --tblout GCF_003403035.1_ASM340303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/reference_markers.hmm GCF_003403035.1_ASM340303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:35,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:35,585] [INFO] Found 6/6 markers.
[2024-01-24 12:34:35,625] [INFO] Query marker FASTA was written to GCF_003403035.1_ASM340303v1_genomic.fna/markers.fasta
[2024-01-24 12:34:35,625] [INFO] Task started: Blastn
[2024-01-24 12:34:35,625] [INFO] Running command: blastn -query GCF_003403035.1_ASM340303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/reference_markers.fasta -out GCF_003403035.1_ASM340303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:36,426] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:36,430] [INFO] Selected 31 target genomes.
[2024-01-24 12:34:36,431] [INFO] Target genome list was writen to GCF_003403035.1_ASM340303v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:36,444] [INFO] Task started: fastANI
[2024-01-24 12:34:36,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0b02da-66f5-4e99-b670-c0d6d4895bbe/GCF_003403035.1_ASM340303v1_genomic.fna.gz --refList GCF_003403035.1_ASM340303v1_genomic.fna/target_genomes.txt --output GCF_003403035.1_ASM340303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:35:06,310] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:06,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:35:06,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:35:06,338] [INFO] Found 31 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:35:06,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:35:06,339] [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 denitrificans	strain=LA-28	GCA_003403035.1	2294114	2294114	type	True	100.0	1437	1437	95	conclusive
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.951	350	1437	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.9333	374	1437	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	77.9097	382	1437	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	77.8023	349	1437	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	77.797	348	1437	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.7956	365	1437	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.7748	389	1437	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	77.7715	349	1437	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.7584	386	1437	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	77.7565	364	1437	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	77.7539	381	1437	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	77.7435	381	1437	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	77.724	383	1437	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	77.7114	386	1437	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	77.7056	351	1437	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	77.68	349	1437	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	77.6731	340	1437	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.6706	357	1437	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	77.6575	361	1437	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.6143	406	1437	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	77.5311	294	1437	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	77.4582	364	1437	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3557	363	1437	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.343	267	1437	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.343	267	1437	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.1997	263	1437	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.1745	252	1437	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.6155	74	1437	95	below_threshold
Paracoccus litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	76.1069	85	1437	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	76.048	75	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:35:06,340] [INFO] DFAST Taxonomy check result was written to GCF_003403035.1_ASM340303v1_genomic.fna/tc_result.tsv
[2024-01-24 12:35:06,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:35:06,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:35:06,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/checkm_data
[2024-01-24 12:35:06,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:35:06,382] [INFO] Task started: CheckM
[2024-01-24 12:35:06,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003403035.1_ASM340303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003403035.1_ASM340303v1_genomic.fna/checkm_input GCF_003403035.1_ASM340303v1_genomic.fna/checkm_result
[2024-01-24 12:35:47,850] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:47,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:47,871] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:47,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:47,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003403035.1_ASM340303v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:47,873] [INFO] Task started: Blastn
[2024-01-24 12:35:47,873] [INFO] Running command: blastn -query GCF_003403035.1_ASM340303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bef60cb-ef22-4ae5-90d5-8b22b989dd4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003403035.1_ASM340303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:49,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:49,230] [INFO] Selected 31 target genomes.
[2024-01-24 12:35:49,231] [INFO] Target genome list was writen to GCF_003403035.1_ASM340303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:49,254] [INFO] Task started: fastANI
[2024-01-24 12:35:49,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d0b02da-66f5-4e99-b670-c0d6d4895bbe/GCF_003403035.1_ASM340303v1_genomic.fna.gz --refList GCF_003403035.1_ASM340303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003403035.1_ASM340303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:19,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:19,829] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:19,829] [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_003403035.1	s__Mesorhizobium_G denitrificans	100.0	1437	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_G	95.0	99.59	99.59	0.91	0.91	2	conclusive
GCF_006440735.1	s__Mesorhizobium sp006440735	78.0418	394	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004963905.1	s__Mesorhizobium sp004963905	77.9181	386	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	77.9106	382	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	77.8155	364	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	77.7925	350	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022705.2	s__Mesorhizobium sp004022705	77.7715	374	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.85	98.91	0.98	0.93	18	-
GCF_003952505.1	s__Mesorhizobium sp003952505	77.7686	352	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_000472705.1	s__Mesorhizobium erdmanii	77.7584	365	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	-
GCF_001427285.1	s__Mesorhizobium sp001427285	77.7093	320	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236565.1	s__Pseudaminobacter alhagi	77.6893	348	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004020545.1	s__Mesorhizobium sp004020545	77.6889	388	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_003353565.1	s__Mesorhizobium sp003353565	77.6826	401	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350085.1	s__Mesorhizobium metallidurans	77.6617	358	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843825.1	s__Mesorhizobium silamurunense	77.6581	361	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_018555685.1	s__Aminobacter anthyllidis	77.6367	368	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	77.6245	385	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427025.1	s__Mesorhizobium sp001427025	77.6129	341	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013170705.1	s__Mesorhizobium loti_D	77.5986	371	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
GCF_003997495.1	s__Mesorhizobium sp003997495	77.5691	389	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963455.1	s__Mesorhizobium sp003963455	77.5581	280	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	77.5501	295	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756535.1	s__Mesorhizobium sp016756535	77.5498	372	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	77.5396	392	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_014863355.1	s__Aminobacter carboxidus	77.5365	361	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	77.438	294	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749525.1	s__Im94 sp009749525	77.4104	247	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Im94	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	77.2776	261	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	77.224	239	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	77.19	263	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:36:19,831] [INFO] GTDB search result was written to GCF_003403035.1_ASM340303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:19,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:19,836] [INFO] DFAST_QC result json was written to GCF_003403035.1_ASM340303v1_genomic.fna/dqc_result.json
[2024-01-24 12:36:19,836] [INFO] DFAST_QC completed!
[2024-01-24 12:36:19,836] [INFO] Total running time: 0h1m59s