error: could not open input file /geneInfo.tab

[Shaunak Adkar]

Hi Alex,

This seems to be the same problem Ezhil was having. Here are some more details. I am running STAR 2.7.11a. The genome generate seems to work fine. When I attempt to align reads, I get the following error: Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab

This is the output at the end of the log file:

Genome: size given as a parameter = 3215411168

SA: size given as a parameter = 24935534806

SAindex: size given as a parameter = 1

Read from SAindex: pGe.gSAindexNbases=14  nSAi=357913940

nGenome=3215411168;  nSAbyte=24935534806

GstrandBit=32   SA number of indices=6044978134

Shared memory is not used for genomes. Allocated a private copy of the genome.

Genome file size: 3215411168 bytes; state: good=1 eof=0 fail=0 bad=0

Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3215411168 bytes

SA file size: 24935534806 bytes; state: good=1 eof=0 fail=0 bad=0

Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24935534806 bytes

Loading SAindex ... done: 1565873619 bytes

Finished loading the genome: Thu Sep  7 17:58:50 2023

Sum of all Genome bytes: 5349899816

Sum of all SA bytes: 3114825160665

Sum of all SAi bytes: 184954821413

Processing splice junctions database sjdbN=383200,   pGe.sjdbOverhang=100

To accommodate alignIntronMax=1000000 redefined winBinNbits=18

To accommodate alignIntronMax=1000000 and alignMatesGapMax=1000000, redefined winFlankNbins=4 and winAnchorDistNbins=8

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

Sep 07 17:58:52 ...... FATAL ERROR, exiting 

Thanks

Shaunak

[Alexander Dobin]

Hi Shaunak,

did you use GTF file when generating the genome index?