genomeParameters.txt missing

[Diksha Marwaha]

Hi, I am trying to run STAR-2.7.11b which is the latest version of STAR alignment tool.  I have tried and done all the troubleshooting steps to solve this error saying while doing alignment step:                                                                                                                               STAR version: 2.7.11b   compiled: 2024-03-13T14:46:00+05:30 :/home/diksham/lipogenesis/myenv/STAR-2.7.11b/source

Mar 16 13:15:58 ..... started STAR run
Mar 16 13:15:58 ..... loading genome
EXITING because of FATAL ERROR: could not open genome file genomeDir//genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permissions.  my command is:  /home/diksham/lipogenesis/myenv/STAR-2.7.11b/STAR --genomeDir genomeDir --sjdbGTFfile gencode_annotation.gtf --readFilesIn /home/diksham/lipogenesis/myenv/Trimmomatic-0.39/paired_files/SRR23529085_forward_paired.fastq.gz /home/diksham/lipogenesis/myenv/Trimmomatic-0.39/paired_files/SRR23529085_reverse_paired.fastq.gz --readFilesCommand zcat

        /home/diksham/lipogenesis/myenv/STAR-2.7.11b/STAR --genomeDir genomeDir --sjdbGTFfile gencode_annotation.gtf --readFilesIn /home/diksham/lipogenesis/myenv/Trimmomatic-0.39/paired_files/SRR23529085_forward_paired.fastq.gz /home/diksham/lipogenesis/myenv/Trimmomatic-0.39/paired_files/SRR23529085_reverse_paired.fastq.gz --readFilesCommand zcat   please help me to solve this why this error is coming. the list of index files generated are:  diksham@iiitd:~/lipogenesis/myenv/STAR-2.7.11b$ cd /home/diksham/lipogenesis/myenv/STAR-2.7.11b/genomeDir
diksham@iiitd:~/lipogenesis/myenv/STAR-2.7.11b/genomeDir$ ls -l
total 21208076
-rw-rw-r-- 1 diksham diksham       3021 Mar 15 20:48 chrLength.txt
-rw-rw-r-- 1 diksham diksham      11672 Mar 15 20:48 chrNameLength.txt
-rw-rw-r-- 1 diksham diksham       8651 Mar 15 20:48 chrName.txt
-rw-rw-r-- 1 diksham diksham       4990 Mar 15 20:48 chrStart.txt
-rw-rw-r-- 1 diksham diksham   58705461 Mar 15 20:48 exonGeTrInfo.tab
-rw-rw-r-- 1 diksham diksham   24161732 Mar 15 20:48 exonInfo.tab
-rw-rw-r-- 1 diksham diksham    2647889 Mar 15 20:48 geneInfo.tab
-rw-rw-r-- 1 diksham diksham      42890 Mar 16 00:26 Log.out
-rw-rw-r-- 1 diksham diksham 7233117440 Mar 15 23:15 SA_0
-rw-rw-r-- 1 diksham diksham 7160908992 Mar 15 23:07 SA_1
-rw-rw-r-- 1 diksham diksham 7207608920 Mar 16 00:26 SA_2
-rw-rw-r-- 1 diksham diksham   12818126 Mar 15 20:48 sjdbList.fromGTF.out.tab
-rw-rw-r-- 1 diksham diksham   16992166 Mar 15 20:48 transcriptInfo.tab

[Brian Haas]

Hi,

Please make sure you have a ctat genome lib installed, preferably the plug-n-play version: https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix

and use this with STAR-Fusion.  

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