Answers.Body: <p>You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of RAM, likely more like 60GB. Also, make sure to look for error messages.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-24T21:36:35.697Z
Answers.Text: qsub -pe threaded 4 -hard -l mem_free=60G -l h_vmem=80G -l mem_token=60G RunSTARIndex.sh...do you think this much is enough, although one node has 128GB....hope this time it will....me running now...Thanks a million in advance...
Answers.UserDisplayName: San
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Answers.CreationDate: 2018-07-24T22:50:28.420Z
Answers.Text: Thanks for the information, I do run the same but it seems, its terminating and giving the same output files. ..this is what I tried in the last ...qsub -pe threaded 4-20 -hard -l mem_free=100G -l h_vmem=120G -l mem_token=60G RunSTARIndex2.sh....Each Node -128 RAM, is their other possible way to Index it?
Answers.UserDisplayName: San
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-25T06:44:48.333Z
Answers.Text: Some genomes require gobs of memory. If you point me to the files you're trying to index I can try and do that for you.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-25T14:42:37.640Z
Answers.Text: Thanks a million Devon Ryan, I tried all possible way to increase memory like ....qsub -pe threaded 4-20 -hard -l mem_free=400G -l h_vmem=560G -l mem_token=80G RunSTARIndex2.sh, but still fail, I don't see any error message, its seems like it terminate on the half way...Could you let me know your email, My be I will email the same to you.
Answers.UserDisplayName: San
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-25T14:49:17.917Z
Answers.Text: Genome Indexing for Xenopus leaves, v9.2, here is the link for the database http://www.xenbase.org/other/static/ftpDatafiles.jsp, Please let me know, if you can  do the indexing for it, Let me know, how I can transfer the index file too, thanks a million in advance ...
Answers.UserDisplayName: San
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-24T20:34:02.077Z
Answers.LastActivityDate: 2018-07-24T20:34:02.077Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file.</p>
  
  <p>Genome size is 3GB, here is the file output</p>
  
  <pre><code>chrLength.txt
  chrNameLength.txt
  chrName.txt
  chrStart.txt
  genomeParameters.txt
  </code></pre>
  
  <p>I have another small Genome 60MB in size, I did the genome indexing, here is the file output</p>
  
  <pre><code>chrLength.txt
  chrNameLength.txt
  chrName.txt
  chrStart.txt
  exonGeTrInfo.tab
  exonInfo.tab
  geneInfo.tab
  Genome
  genomeParameters.txt
  SA
  SAindex
  sjdbInfo.txt
  sjdbList.fromGTF.out.tab
  sjdbList.out.tab
  transcriptInfo.tab
  </code></pre>
  
  <p>My point here is that, why I got the extra information for my small genome size, but I didn't get the same for the big size genome. I do apply the same procedure for the both.</p>
  
  <p>here is the below information. Only difference I made for the large Genome size is (<code>--sjdbOverhang 99 --genomeChrBinNbits 15</code>) to reduce the memory, but the rest of things are same for small genome.</p>
  
  <pre><code>#!/bin/bash
  NUM_THREADS=12
  mkdir DB
  STAR --runMode genomeGenerate --genomeDir DB \
      --runThreadN $NUM_THREADS \
      --genomeFastaFiles XL9_2.fa \
      --sjdbGTFfile XENLA_Frog.gtf+gff3 \
      --sjdbOverhang 99 \
      --genomeChrBinNbits 15
  </code></pre>
  
  <p>Could anyone give an idea, why there is different, I am new to this field, so I am wondering about the difference in this.</p>
  
  <p>Thanks in advance.</p>
  
  <p>Cheer
  San</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-25T13:20:30.067Z
Comments.Text: The files missing in the case of the larger genome are the actual index itself - it doesn't look like STAR completed. Do you have STDOUT/STDERR from the runs?
Comments.UserDisplayName: sjcockell
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-25T14:43:58.830Z
Comments.Text: Here is my below syntax, I use it for It                                                     #!/bin/bash
  module load star/2.5.0c
  
  NUM_THREADS=22
  
  mkdir Sangv92db
  STAR --runMode genomeGenerate --genomeDir Sangv92db \
      --runThreadN $NUM_THREADS \
      --genomeFastaFiles /ifs/home/skm9/san/xlaevis/XL9_2.fa \
      --sjdbGTFfile /ifs/home/skm9/san/xlaevis/XENLA_9.2_Xenbase.gff3
      --sjdbOverhang 99 \
      --genomeChrBinNbits 15,                                                                                                It run and gene the files out same like the above I mentioned.
Comments.UserDisplayName: San
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-25T14:47:25.700Z
Comments.Text: here is the memory allocation I used for it, still not able to complete the indexing, ... qsub -pe threaded 4-20 -hard -l mem_free=400G -l h_vmem=560G -l mem_token=80G RunSTARIndex2.sh...
Comments.UserDisplayName: San
Tags: <genome><reference-genome><star><genome-index>
Title: STAR Indexing Diference for Small and Large Genome File Output
ThreadText: # STAR Indexing Diference for Small and Large Genome File Output
  
  (Asked by: username_0 on 2018-07-24)
  
  I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file.
  
  Genome size is 3GB, here is the file output
  
  ```
  chrLength.txt
  chrNameLength.txt
  chrName.txt
  chrStart.txt
  genomeParameters.txt
  
  ```
  
  I have another small Genome 60MB in size, I did the genome indexing, here is the file output
  
  ```
  chrLength.txt
  chrNameLength.txt
  chrName.txt
  chrStart.txt
  exonGeTrInfo.tab
  exonInfo.tab
  geneInfo.tab
  Genome
  genomeParameters.txt
  SA
  SAindex
  sjdbInfo.txt
  sjdbList.fromGTF.out.tab
  sjdbList.out.tab
  transcriptInfo.tab
  
  ```
  
  My point here is that, why I got the extra information for my small genome size, but I didn't get the same for the big size genome. I do apply the same procedure for the both.
  
  here is the below information. Only difference I made for the large Genome size is (`--sjdbOverhang 99 --genomeChrBinNbits 15`) to reduce the memory, but the rest of things are same for small genome.
  
  ```
  #!/bin/bash
  NUM_THREADS=12
  mkdir DB
  STAR --runMode genomeGenerate --genomeDir DB \
      --runThreadN $NUM_THREADS \
      --genomeFastaFiles XL9_2.fa \
      --sjdbGTFfile XENLA_Frog.gtf+gff3 \
      --sjdbOverhang 99 \
      --genomeChrBinNbits 15
  
  ```
  
  Could anyone give an idea, why there is different, I am new to this field, so I am wondering about the difference in this.
  
  Thanks in advance.
  
  Cheer
  San
  
  **Tags:** genome, reference-genome, star, genome-index
  
  > **Comments:**
  > **username_1**: The files missing in the case of the larger genome are the actual index itself - it doesn't look like STAR completed. Do you have STDOUT/STDERR from the runs?  
  > **username_0**: Here is my below syntax, I use it for It                                                     #!/bin/bash module load star/2.5.0c  NUM_THREADS=22  mkdir Sangv92db STAR --runMode genomeGenerate --genomeDir Sangv92db \     --runThreadN $NUM_THREADS \     --genomeFastaFiles /ifs/home/skm9/san/xlaevis/XL9_2.fa \     --sjdbGTFfile /ifs/home/skm9/san/xlaevis/XENLA_9.2_Xenbase.gff3     --sjdbOverhang 99 \     --genomeChrBinNbits 15,                                                                                                It run and gene the files out same like the above I mentioned.  
  > **username_0**: here is the memory allocation I used for it, still not able to complete the indexing, ... qsub -pe threaded 4-20 -hard -l mem_free=400G -l h_vmem=560G -l mem_token=80G RunSTARIndex2.sh...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-07-24. Score: 1 | Accepted answer
  
  You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of RAM, likely more like 60GB. Also, make sure to look for error messages.
  
  > **Comments:**
  > **username_0**: qsub -pe threaded 4 -hard -l mem_free=60G -l h_vmem=80G -l mem_token=60G RunSTARIndex.sh...do you think this much is enough, although one node has 128GB....hope this time it will....me running now...Thanks a million in advance...  
  > **username_0**: Thanks for the information, I do run the same but it seems, its terminating and giving the same output files. ..this is what I tried in the last ...qsub -pe threaded 4-20 -hard -l mem_free=100G -l h_vmem=120G -l mem_token=60G RunSTARIndex2.sh....Each Node -128 RAM, is their other possible way to Index it?  
  > **username_2**: Some genomes require gobs of memory. If you point me to the files you're trying to index I can try and do that for you.  
  > **username_0**: Thanks a million username_2 username_2, I tried all possible way to increase memory like ....qsub -pe threaded 4-20 -hard -l mem_free=400G -l h_vmem=560G -l mem_token=80G RunSTARIndex2.sh, but still fail, I don't see any error message, its seems like it terminate on the half way...Could you let me know your email, My be I will email the same to you.  
  > **username_0**: Genome Indexing for Xenopus leaves, v9.2, here is the link for the database http://www.xenbase.org/other/static/ftpDatafiles.jsp, Please let me know, if you can  do the indexing for it, Let me know, how I can transfer the index file too, thanks a million in advance ...  
  
  ---
  
  