[2024-01-25 19:52:05,634] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:05,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:05,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference
[2024-01-25 19:52:06,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:06,870] [INFO] Task started: Prodigal
[2024-01-25 19:52:06,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b92c4f3-dd25-4892-9715-feddfee7749c/GCF_017813335.1_ASM1781333v1_genomic.fna.gz | prodigal -d GCF_017813335.1_ASM1781333v1_genomic.fna/cds.fna -a GCF_017813335.1_ASM1781333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:20,299] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:20,299] [INFO] Task started: HMMsearch
[2024-01-25 19:52:20,299] [INFO] Running command: hmmsearch --tblout GCF_017813335.1_ASM1781333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/reference_markers.hmm GCF_017813335.1_ASM1781333v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:20,573] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:20,574] [INFO] Found 6/6 markers.
[2024-01-25 19:52:20,613] [INFO] Query marker FASTA was written to GCF_017813335.1_ASM1781333v1_genomic.fna/markers.fasta
[2024-01-25 19:52:20,613] [INFO] Task started: Blastn
[2024-01-25 19:52:20,613] [INFO] Running command: blastn -query GCF_017813335.1_ASM1781333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/reference_markers.fasta -out GCF_017813335.1_ASM1781333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:21,447] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:21,450] [INFO] Selected 29 target genomes.
[2024-01-25 19:52:21,451] [INFO] Target genome list was writen to GCF_017813335.1_ASM1781333v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:21,495] [INFO] Task started: fastANI
[2024-01-25 19:52:21,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b92c4f3-dd25-4892-9715-feddfee7749c/GCF_017813335.1_ASM1781333v1_genomic.fna.gz --refList GCF_017813335.1_ASM1781333v1_genomic.fna/target_genomes.txt --output GCF_017813335.1_ASM1781333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:53,008] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:53,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:53,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:53,025] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:52:53,025] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:52:53,026] [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
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	79.0529	427	1558	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	78.3367	324	1558	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.2973	373	1558	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.293	401	1558	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.2346	382	1558	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.2328	380	1558	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.2089	384	1558	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	78.1976	383	1558	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	78.1894	376	1558	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	78.1714	415	1558	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	78.1701	398	1558	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.1689	366	1558	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.1197	375	1558	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	78.101	320	1558	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	78.0965	394	1558	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.0753	351	1558	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	78.075	392	1558	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.0608	439	1558	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.0289	377	1558	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	78.0268	365	1558	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	77.9593	362	1558	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.873	385	1558	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	77.8141	342	1558	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.8031	368	1558	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	77.7891	372	1558	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.7751	322	1558	95	below_threshold
Aquamicrobium zhengzhouense	strain=cd-1	GCA_016124105.1	2781738	2781738	type	True	77.6018	212	1558	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	77.4218	302	1558	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	77.3847	289	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:53,027] [INFO] DFAST Taxonomy check result was written to GCF_017813335.1_ASM1781333v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:53,027] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:53,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:53,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/checkm_data
[2024-01-25 19:52:53,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:53,072] [INFO] Task started: CheckM
[2024-01-25 19:52:53,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813335.1_ASM1781333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813335.1_ASM1781333v1_genomic.fna/checkm_input GCF_017813335.1_ASM1781333v1_genomic.fna/checkm_result
[2024-01-25 19:53:33,311] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:33,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:33,351] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:33,351] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:33,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813335.1_ASM1781333v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:33,352] [INFO] Task started: Blastn
[2024-01-25 19:53:33,352] [INFO] Running command: blastn -query GCF_017813335.1_ASM1781333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg071a4de9-87bb-4ecf-96f6-e8db522ec96c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813335.1_ASM1781333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:34,991] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:34,995] [INFO] Selected 19 target genomes.
[2024-01-25 19:53:34,995] [INFO] Target genome list was writen to GCF_017813335.1_ASM1781333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:35,042] [INFO] Task started: fastANI
[2024-01-25 19:53:35,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b92c4f3-dd25-4892-9715-feddfee7749c/GCF_017813335.1_ASM1781333v1_genomic.fna.gz --refList GCF_017813335.1_ASM1781333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813335.1_ASM1781333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:55,749] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:55,761] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:55,761] [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_017813335.1	s__Tianweitania sediminis	100.0	1556	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Tianweitania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014652875.1	s__Corticibacterium populi	79.9717	609	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018457165.1	s__Corticibacterium sp018457165	79.9138	616	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316345.1	s__Corticibacterium sp002316345	79.7941	508	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	78.3905	392	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_003289945.1	s__Mesorhizobium hawassense	78.2328	380	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	78.2218	371	1558	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_003666685.1	s__RCIZ01 sp003666685	78.1817	386	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503535.1	s__Mesorhizobium sp005503535	78.1718	365	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	78.1533	417	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952525.1	s__Mesorhizobium sp002294945	78.1429	350	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.39	99.02	0.88	0.85	8	-
GCF_003148475.1	s__Pseudaminobacter salicylatoxidans	78.0047	382	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_004791025.1	s__Mesorhizobium sp004791025	78.0023	406	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_011045125.1	s__Pseudaminobacter camelthorni	77.9979	385	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	77.9536	362	1558	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_001014615.2	s__Aquamicrobium_A sp001014615	77.9439	392	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	77.8607	342	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	77.8274	381	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_000236565.1	s__Pseudaminobacter alhagi	77.8164	383	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:55,762] [INFO] GTDB search result was written to GCF_017813335.1_ASM1781333v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:55,763] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:55,767] [INFO] DFAST_QC result json was written to GCF_017813335.1_ASM1781333v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:55,767] [INFO] DFAST_QC completed!
[2024-01-25 19:53:55,767] [INFO] Total running time: 0h1m50s