[2024-01-25 18:08:05,575] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:05,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:05,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference
[2024-01-25 18:08:06,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:06,758] [INFO] Task started: Prodigal
[2024-01-25 18:08:06,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc3eb62f-61f0-46e2-8033-3843af865988/GCF_017355985.1_ASM1735598v1_genomic.fna.gz | prodigal -d GCF_017355985.1_ASM1735598v1_genomic.fna/cds.fna -a GCF_017355985.1_ASM1735598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:22,618] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:22,618] [INFO] Task started: HMMsearch
[2024-01-25 18:08:22,618] [INFO] Running command: hmmsearch --tblout GCF_017355985.1_ASM1735598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/reference_markers.hmm GCF_017355985.1_ASM1735598v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:23,018] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:23,019] [INFO] Found 6/6 markers.
[2024-01-25 18:08:23,072] [INFO] Query marker FASTA was written to GCF_017355985.1_ASM1735598v1_genomic.fna/markers.fasta
[2024-01-25 18:08:23,072] [INFO] Task started: Blastn
[2024-01-25 18:08:23,072] [INFO] Running command: blastn -query GCF_017355985.1_ASM1735598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/reference_markers.fasta -out GCF_017355985.1_ASM1735598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:24,004] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:24,007] [INFO] Selected 22 target genomes.
[2024-01-25 18:08:24,007] [INFO] Target genome list was writen to GCF_017355985.1_ASM1735598v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:24,055] [INFO] Task started: fastANI
[2024-01-25 18:08:24,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3eb62f-61f0-46e2-8033-3843af865988/GCF_017355985.1_ASM1735598v1_genomic.fna.gz --refList GCF_017355985.1_ASM1735598v1_genomic.fna/target_genomes.txt --output GCF_017355985.1_ASM1735598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:55,065] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:55,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:55,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:55,078] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:55,078] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:55,078] [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
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	100.0	2148	2148	95	conclusive
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	78.5077	734	2148	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	78.4188	737	2148	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	78.3849	648	2148	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	78.3439	683	2148	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	78.322	736	2148	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	78.3118	693	2148	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	78.3116	725	2148	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	78.3078	697	2148	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	78.1475	688	2148	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	78.1412	644	2148	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	78.0611	634	2148	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.9908	608	2148	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	77.9739	669	2148	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.9717	641	2148	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.9554	681	2148	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	77.7866	683	2148	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	77.7111	618	2148	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	77.2808	426	2148	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	77.0657	424	2148	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.4776	345	2148	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.4602	341	2148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:55,079] [INFO] DFAST Taxonomy check result was written to GCF_017355985.1_ASM1735598v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:55,080] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:55,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:55,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/checkm_data
[2024-01-25 18:08:55,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:55,139] [INFO] Task started: CheckM
[2024-01-25 18:08:55,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017355985.1_ASM1735598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017355985.1_ASM1735598v1_genomic.fna/checkm_input GCF_017355985.1_ASM1735598v1_genomic.fna/checkm_result
[2024-01-25 18:09:45,735] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:45,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:45,756] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:45,756] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:45,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017355985.1_ASM1735598v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:45,757] [INFO] Task started: Blastn
[2024-01-25 18:09:45,757] [INFO] Running command: blastn -query GCF_017355985.1_ASM1735598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6262d6-d697-4f19-91dc-d798d9742bcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_017355985.1_ASM1735598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:47,565] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:47,567] [INFO] Selected 22 target genomes.
[2024-01-25 18:09:47,567] [INFO] Target genome list was writen to GCF_017355985.1_ASM1735598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:47,587] [INFO] Task started: fastANI
[2024-01-25 18:09:47,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3eb62f-61f0-46e2-8033-3843af865988/GCF_017355985.1_ASM1735598v1_genomic.fna.gz --refList GCF_017355985.1_ASM1735598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017355985.1_ASM1735598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:19,055] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:19,068] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:19,069] [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_017355985.1	s__Desertibacter sp017355985	100.0	2148	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Desertibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016806835.1	s__Skermanella rosea	78.5403	731	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	78.4853	691	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	78.4852	630	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	78.4529	731	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	78.4296	715	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_007827815.1	s__Azospirillum brasilense_C	78.3725	686	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_017876155.1	s__Azospirillum rugosum	78.3483	728	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119195.2	s__Azospirillum baldaniorum	78.3229	695	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_003130795.1	s__Azospirillum thermophilum	78.3111	725	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192915.1	s__Azospirillum sp014192915	78.3074	690	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356015.1	s__Azospirillum sp017356015	78.2672	720	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	78.2367	734	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	78.1104	650	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	78.0954	698	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_017876165.1	s__Azospirillum soli	78.072	632	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	77.9661	671	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	77.961	644	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	77.9517	644	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	77.9307	701	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	77.9033	694	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000936425.1	s__Skermanella aerolata	77.7076	618	2148	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:19,070] [INFO] GTDB search result was written to GCF_017355985.1_ASM1735598v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:19,071] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:19,076] [INFO] DFAST_QC result json was written to GCF_017355985.1_ASM1735598v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:19,076] [INFO] DFAST_QC completed!
[2024-01-25 18:10:19,076] [INFO] Total running time: 0h2m14s