Closed kate-simonova closed 3 years ago
While running the command I am getting the error:
for i in $(ls $path_to_fq/ | rev | cut -c 14- | rev | sort -u); do Rscript FuSeq_v1.1.4_linux_x86-64/R/FuSeq.R in=$i txfasta=GRCh37_files/Homo_sapiens.GRCh37.75.cdna.all.fa sqlite=GRCh37_files/Homo_sapiens.GRCh37.75.sqlite txanno=GRCh37_files/Homo_sapiens.GRCh37.75.txAnno.RData out=$folder_name params=FuSeq_v1.1.4_linux_x86-64/R/params.txt done
FOLDER NAME: 26-R-LU2-LI_S2_trim_L001_out During startup - Warning message: Setting LC_CTYPE failed, using "C" Number of arguments: 6 List of arguments: in=26-R-LU2-LI_S2_trim_L001 txfasta=GRCh37_files/Homo_sapiens.GRCh37.75.cdna.all.fa sqlite=GRCh37_files/Homo_sapiens.GRCh37.75.sqlite txanno=GRCh37_files/Homo_sapiens.GRCh37.75.txAnno.RData out=26-R-LU2-LI_S2_trim_L001_out params=FuSeq_v1.1.4_linux_x86-64/R/params.txt ----- Parameter settings: readStrands= UN chromRef=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y maxSharedCount= 0.05 onlyProteinCodingGenes= TRUE minGeneDist= 1e+05 minJunctionDist= 1e+05 maxInvertedFusionCount= 0 maxMRfusionFc= 2 maxMRfusionNum= 2 sgtMRcount= 10 minMR= 2 minNonDupMR= 2 minSR= 1 minScore= 3 exonBoundary= TRUE keepRData= TRUE exportFasta= FALSE ------------------------- ------------------------------------------------------------------ Processing mapped reads (MR) from dataset: 26-R-LU2-LI_S2_trim_L001 read strands: UN Read fusion equivalence classes Reading 26-R-LU2-LI_S2_trim_L001/feq_UN.txt The total number of fusion equivalence classes: 0 ------------------------------------------------------------------ Processing split reads (SR) from dataset: 26-R-LU2-LI_S2_trim_L001 read strands: UN Get split reads ...Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: processSplitRead -> read.csv -> read.table In addition: Warning messages: 1: In max(feqR$Feq) : no non-missing arguments to max; returning -Inf 2: In min(fragRg) : no non-missing arguments to min; returning Inf 3: In max(fragRg) : no non-missing arguments to max; returning -Inf Execution halted
I solved the problem the mistake was in the previous command I was looping for not existing fastq files.
While running the command I am getting the error: