Encode miRNA-Seq analysis pipeline - *INPUT FILE* error: could not open input file /geneInfo.tab

[Ezhil A]

Hi,

I am trying to run the Encode miRNA-Seq analysis pipeline. I have generated the STAR Index, and it created all files without any issues. When I tried to run the alignment with our fastq files, it says

Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab
Solution: check that the file exists and you have read permission for this file
          SOLUTION: utilize --sjdbGTFfile /path/to/annotations.gtf option at the genome generation step or mapping step

Strangely, I have the file 'geneInfo.tab' under the genomeDir directory and have the read permission. Could you please help me to fix this issue?

I am using the following command:

/usr/local/bin/STAR --genomeDir /Users/mszaal/TOOLS/rna_seq/genomeDir --readFilesIn /Users/mszaal/Trimmed_files/31042-001.R1.trimmed.fastq --runThreadN 4 --sjdbGTFfile /Users/mszaal/TOOLS/rna_seq/encode_annotation/gencode.v29.primary_assembly.annotation.mirnas.gtf --alignEndsType EndToEnd --outFilterMismatchNmax 1 --outFilterMultimapScoreRange 0 --quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 10 --outSAMunmapped Within --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --outFileNamePrefix /Users/mszaal/Aligned_files/31042-001.R1.

Many thanks,

Ezhil

[Alexander Dobin]

Hi Ezhil,

please send me the Log.out file.