Error: Please be sure to use the STAR aligner with min version: 2.6.1 #104
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Hi,
When generating the chimeric junction file by running the latest version of
STAR, it's important to include the new STAR parameter:
…--chimOutJunctionFormat 1
In order to proceed, you'd have to rerun STAR this way, or to run STAR as
part of the STAR-Fusion run (and STAR-Fusion will include the parameter on
its own). Otherwise, you'll need to use an earlier version of STAR-Fusion
that's compatible with the current junction file you're working with.
best,
~b
On Mon, Oct 29, 2018 at 1:53 PM Komal Rathi ***@***.***> wrote:
Hi,
I have installed STAR and STAR-Fusion like this:
conda install -c bioconda star
STAR --version
STAR_2.6.1a_08-27
conda install -c bioconda star-fusion
STAR-Fusion --version
STAR-Fusion version: 1.5.0
Now when I am trying to run STAR-Fusion using this command, it is throwing
an error like this Please be sure to use the STAR aligner with min
version: 2.6.1 :
# command
$ /mnt/isilon/cbmi/variome/rathik/tools/miniconda3/envs/pdx-subtract-env/bin/STAR-Fusion --CPU 4 --genome_lib_dir /mnt/isilon/cbmi/variome/reference/star_fusion_db/hg19/GRCh37_v19_CTAT_lib_Feb092018/ctat_genome_lib_build_dir -J /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/realign/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_Chimeric.out.junction --left_fq /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/bam/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_hybrid_hg19_1_sequence.txt.bz2 --right_fq /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/bam/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_hybrid_hg19_2_sequence.txt.bz2 --output_dir /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/starfusion/PPTC-AF03-XTP1-A-1-0-R/ --FusionInspector inspect --examine_coding_effect --denovo_reconstruct
# logs
CMD: mkdir -p /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/starfusion/PPTC-AF03-XTP1-A-1-0-R//_starF_checkpoints
CMD: mkdir -p /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/starfusion/PPTC-AF03-XTP1-A-1-0-R//star-fusion.preliminary
Error, file: /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/realign/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_Chimeric.out.junction doesn't have expected formatting. Please be sure to use the STAR aligner with min version: 2.6.1 at /mnt/isilon/cbmi/variome/rathik/tools/miniconda3/envs/pdx-subtract-env/lib/STAR-Fusion/STAR-Fusion line 1023.
main::get_num_total_rnaseq_frags("/mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_"...) called at /mnt/isilon/cbmi/variome/rathik/tools/miniconda3/envs/pdx-subtract-env/lib/STAR-Fusion/STAR-Fusion line 521
I checked the STAR version of Chimeric.out.junction, it was generated
using STAR_2.6.1a:
$ head /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/realign/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_Log.out
STAR version=STAR_2.6.1a
STAR compilation time,server,dir=Tue Aug 14 18:24:22 EDT 2018 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.master/source
##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 1
runDirPerm User_RWX
And these are the first few lines of Chimeric.out.junction file:
$ head /mnt/isilon/maris_lab/target_nbl_ngs/PPTC-PDX-genomics/mouse_subtraction_pipeline/rna-hybrid/results/realign/PPTC-AF03-XTP1-A-1-0-R/PPTC-AF03-XTP1-A-1-0-R_Chimeric.out.junction
16 67903270 - 1 23649028 + 0 0 0 HWI-ST1353:652:CBK13ACXX:3:1110:20131:97655 67903271 74S27M 23649029 27S74M-1p101M
1 23650226 + 1 23650207 - 2 6 1 HWI-ST1353:652:CBK13ACXX:3:1201:4740:96246 23650049 2S99M6p72M29S 23650180 2S27M72S
1 23662805 + 1 23661033 + 0 0 1 HWI-ST1353:652:CBK13ACXX:3:1210:13283:52854 23662745 60M41S 23661034 60S41M4p101M
1 23662811 + 1 23661017 + 0 0 2 HWI-ST1353:652:CBK13ACXX:3:2208:2110:31207 23662706 101M-46p50M51S 23661018 50S51M
1 23829116 + 1 23829012 + 0 0 3 HWI-ST1353:652:CBK13ACXX:3:1114:1385:58053 23829087 29M72S 23829013 29S72M-28p101M
1 23833129 + 1 23833137 - 0 0 8 HWI-ST1353:652:CBK13ACXX:3:1210:2477:75249 23832970 101M-2p60M41S 23833096 41M60S
1 23833278 + 1 23833157 + 2 3 0 HWI-ST1353:652:CBK13ACXX:3:2303:13084:88134 23833244 34M67S 23833158 34S67M-46p101M
1 23833299 + 1 23833356 - 0 0 4 HWI-ST1353:652:CBK13ACXX:3:1111:5865:95158 23833113 101M12p73M28S 23833328 28M73S
1 23833291 + 1 23833089 + 0 0 3 HWI-ST1353:652:CBK13ACXX:3:2212:6473:100436 23833060 101M72p58M43S 23833090 58S43M
1 23833475 + 1 23833503 - 0 0 5 HWI-ST1353:652:CBK13ACXX:3:2106:12484:8905 23833366 101M-54p62M38S 23833465 38M63S
Please advise. Thanks!
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http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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Hi,
I have installed STAR and STAR-Fusion like this:
Now when I am trying to run STAR-Fusion using this command, it is throwing an error:
Please be sure to use the STAR aligner with min version: 2.6.1:I checked the STAR version of Chimeric.out.junction, it was generated using
STAR_2.6.1a:And these are the first few lines of Chimeric.out.junction file:
When I downgrade STAR-Fusion to 1.4.0, it seems to be working though. Would I need to re-align the files using the latest version of STAR?
Please advise. Thanks!
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