Question: could not open genomeParameters.txt
1
gravatar for yueli7
15 months ago by
yueli740
China
yueli740 wrote:

Hello,

By using STAR, I have already successfully generated genome indexes.

Apr 26 05:20:22 ..... finished successfully

Then I try to running mapping.

It said could not find open genome file. Actually, genomeParameters.txt was in my folder genomeDir.

Thanks in advance for great help!

yue

./STAR --runThreadN 30 --readFilesCommand gunzip -c --readFilesIn /home/administrator/human/549_S124_L008_R1_001.fastq.gz /home/administrator/human/549_S124_
Apr 26 06:53:21 ..... started STAR run
Apr 26 06:53:21 ..... 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 permsissions
rna-seq software error • 800 views
ADD COMMENTlink modified 15 months ago by RamRS22k • written 15 months ago by yueli740
1

While it is tempting to ask a question here for an easy answer if you look at the ERROR in your post above it is giving you a good idea of what is wrong. If your try/search/fix the error on your own (there should be plenty of resources available on net) you will benefit most in the long run rather than us giving you an answer.

That said you are always welcome to ask questions and tell us what you tried to do for a fix if it does not work.

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax69k

There is also a SOLUTION part that lists almost all possible solutions to this problem. Agree that OP needs to try and solve it themselves.

ADD REPLYlink written 15 months ago by RamRS22k

Thank you!

--genomeDir /path/to/STARgenomeIndex/

ADD REPLYlink written 15 months ago by yueli740

Please edit the original post. Take out the extraneous info noted by @h.mon below and make sure the complete command is posted there.

ADD REPLYlink modified 15 months ago • written 15 months ago by genomax69k

I've removed it as it has some sensitive info.

ADD REPLYlink written 15 months ago by RamRS22k
./STAR --runThreadN 12 --genomeDir /home/administrator/genomeDir --readFilesCommand gunzip -c --readFilesIn /home/administrator/human/549_S124_L008_R1_001.fastq.gz /home/administrator/human/549_S124_L008_R2_001.fastq.gz  --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /home/administrator/human/23 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20
Apr 26 07:30:27 ..... started STAR run
Apr 26 07:30:27 ..... loading genome
Apr 26 07:32:09 ..... started mapping
Apr 26 07:51:49 ..... started sorting BAM
Apr 26 07:59:00 ..... finished successfully
ADD REPLYlink modified 15 months ago by RamRS22k • written 15 months ago by yueli740

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time. Formatting bar

Also, I've removed your username, hostname and pwd from the command you posted. That is unnecessary information, please do not post it again.

ADD REPLYlink written 15 months ago by RamRS22k

Thank you so much for your help!

ADD REPLYlink written 15 months ago by yueli740

yueli7 : Looks like all is well.

ADD REPLYlink written 15 months ago by genomax69k
1

There is no need to include [redacted-username]@[redacted-hostname]:~/STAR-2.6.0a/source$ in you code output, it just adds clutter. And you ./STAR command-line is incomplete, it gets interrupted at /home/administrator/human/549_S124_.

ADD REPLYlink modified 15 months ago by RamRS22k • written 15 months ago by h.mon26k

I've removed (redacted) quasi-sensitive parts of OP's command prompt.

ADD REPLYlink written 15 months ago by RamRS22k
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