Error running FuSeq.R
kate-simonova opened this issue · comments
Rscript FuSeq.R in=/home/me/test_output txfasta=/home/me/Homo_sapiens.GRCh38.cdna.all.fa sqlite=/home/me/Homo_sapiens.GRCh38.103.sqlite txanno=/home/me/Homo_sapiens.GRCh38.94.txAnno.RData out=/home/me/Out params=/home/me/FuSeq_v1.1.4_linux_x86-64/R/params.txt
txann was downloaded from the github page
txfasta was downloaded from ensembl web-page along woth gft file used to build a db sqlite
Results in the following Error:
List of arguments: in=/home/me/test_output txfasta=/home/me/Homo_sapiens.GRCh38.cdna.all.fa sqlite=/home/me/Homo_sapiens.GRCh38.103.sqlite txanno=/home/me/Homo_sapiens.GRCh38.94.txAnno.RData out=/home/me/Out params=/home/me/FuSeq_v1.1.4_linux_x86-64/R/params.txt
Warning: The output directory is already existed, old results will be over written
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Parameter settings:
readStrands= UN
chromRef=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
maxSharedCount= 0.05
onlyProteinCodingGenes= TRUE
minGeneDist= 1e+05
minJunctionDist= 1e+05
maxInvertedFusionCount= 0
maxMRfusionFc= 2
maxMRfusionNum= 2
sgtMRcount= 10
minMR= 2
minNonDupMR= 2
minSR= 1
minScore= 3
exonBoundary= TRUE
keepRData= TRUE
exportFasta= FALSE
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Processing mapped reads (MR) from dataset: /home/me/test_output read strands: UN
Read fusion equivalence classes
Reading /home/me/test_output/feq_UN.txt
The total number of fusion equivalence classes: 1161
Create the maps between feq and fgeError in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'TXNAME'. Please use the keys method to see a listing of valid arguments.
Calls: processMappedRead ... select -> .select -> testSelectArgs -> .testForValidKeys
Execution halted
I solved the issue myself the problem was that I used GRCh38 and I did.t notice in README the following lines:
Homo sapiens version GRCh38.94: However, before running FuSeq for this annotation, users should clean the version information from the transcript names and gene names as described in Section 7.