STAR- error
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4 weeks ago
carolgalah • 0

Hi.

I'm trying using aligner STAR, with the follow scprit:

/opt/STAR-2.7.9a/bin/Linux_x86_64/STAR \
  --genomeDir /home/julia.nicoliello/genome_index \
  --readFilesCommand zcat \
  --readFilesIn /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R1_001.fastq.gz /home/julia.nicoliello/fastq-files/Giselle_S13_L002_R2_001.fastq.gz \
  --outFileNamePrefix /home/julia.nicoliello/resultado_star \
  --outFilterType BySJout \
  --outSAMunmapped Within \
  --outSAMtype BAM SortedByCoordinate \
  --outSAMattrIHstart 0 \
  --outFilterIntronMotifs RemoveNoncanonical \
  --runThreadN 20 \
  --quantMode TranscriptomeSAM \
  --outWigType bedGraph \
  --outWigStrand Stranded

But, I have error 109, with this message:

BAMoutuput.cpp27:BAMoutput: existing because "OUTPUT file" error: could not create output file /home/julia.nicoliello/resultado_star/Giselle/Giselle_STARtmp/BAMsort/19/28
Solution: check that the path exists and you have write permission for this file. Also check unlimit -n and increase it to allow more open files.

I believe the STAR starting, but stop because the error. the paths resultado_star and resultado_STARtmp were created, but the process is not finalized.

I have checked the permission and it's ok for all paths. I don't know the problem!

Thanks,

STAR gene RNA-Seq • 298 views
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Try reducing the number of threads to 8. Also, please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
code_formatting

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Thanks Ram!

But threads to 8 will be enough to cover the human genome? I mean, it's not slow?

Thanks

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It might be slow, but it'll at least run to completion. You can try upping the threads from there for subsequent samples if it runs to completion. Plus, given that you're trying to get sorted BAMs, you'll need to give it a whole bunch of memory or use the appropriate parameter to limit BAM sorting RAM (I recommend this option).

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I am a bit confused since the path in your error message does not correspond to the path you specified in the command you posted.

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Yes. It's true! I'll check for this... thanks

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