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cougarlj / COMPSRA

COMPSRA: a COMprehensive Platform for Small RNA-Seq data Analysis
https://regepi.bwh.harvard.edu/circurna/
GNU General Public License v3.0
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Missing genomeParameters.txt in the Alginment module #32

Open obalasz opened 2 years ago

obalasz commented 2 years ago

Hi,

I used the pipeline on our data, but unfortunatelly I've encountered with this error message: How Can I create the database?

+++++++++++++++++++++++++++++++

14:24:55.229 [pool-3-thread-1] INFO java.lang.Class - To run: ..../COMPSRA/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runThreadN 4 --runMode alignReads --outSAMtype BAM Unsorted --outSAMattributes Standard --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped None --alignEndsType Local --outFilterMismatchNmax 1 --alignIntronMax 1 --alignIntronMin 2 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMultimapNmax 1000000 --genomeDir ..../COMPSRA/bundle_v1/db/star/hg38 --readFilesIn ..../COMPSRA/ssample_example_out/ssample/ssample_17to75_FitRead.fastq.gz --outFileNamePrefix ..../COMPSRA/ssample_example_out/ssample/ssample_17to75_FitReadSTAR

Feb 24 14:24:55 ..... started STAR run Feb 24 14:24:55 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file ..../COMPSRA/bundle_v1/db/star/hg38/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

Feb 24 14:24:55 ...... FATAL ERROR, exiting Fail to call: ..../COMPSRA/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runThreadN 4 --runMode alignReads --outSAMtype BAM Unsorted --outSAMattributes Standard --readFilesCommand zcat --outSAMunmapped Within --outReadsUnmapped None --alignEndsType Local --outFilterMismatchNmax 1 --alignIntronMax 1 --alignIntronMin 2 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterMultimapNmax 1000000 --genomeDir ..../COMPSRA/bundle_v1/db/star/hg38 --readFilesIn ..../COMPSRA/ssample_example_out/ssample/ssample_17to75_FitRead.fastq.gz --outFileNamePrefix ..../COMPSRA/ssample_example_out/ssample/ssample_17to75_FitReadSTAR

14:24:55.294 [main] INFO edu.harvard.channing.compass.core.Produce - Alignment module was completed.

hafizmtalha commented 2 years ago

looks like your star indexing command didn't work. did u enable -mbi parameter in the command ?

cougarlj commented 2 years ago

Dear obalasz,

Sorry to reply late. When you use COMPSRA for the first time, please add "-mbi" after "-aln" and this will tell STAR to build the genome index file (like SA files). It will cost several hours for hg38. Or you can build the genome index by yourself and copy to bundle. For the running afterwards, there is no need to add "-mbi" in the command line.

Best Wishes, Jiang Li

obalasz commented 2 years ago

Hi,

thank you very much, now It's working like a charm! :) May I recommend adding this info as a comment to the manual?

Cheers, Balázs

cougarlj @.***> ezt írta (időpont: 2022. márc. 9., Sze, 2:18):

Dear obalasz,

Sorry to reply late. When you use COMPSRA for the first time, please add "-mbi" after "-aln" and this will tell STAR to build the genome index file (like SA files). It will cost several hours for hg38. Or you can build the genome index by yourself and copy to bundle. For the running afterwards, there is no need to add "-mbi" in the command line.

Best Wishes, Jiang Li

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cougarlj commented 2 years ago

Dear obalasz,

Sure! Welcome to use COMPSRA and cite our paper (PMID: 32165660).

Best Wishes, Jiang Li