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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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Problem with alignment using hg19 #9

Closed drumair closed 3 years ago

drumair commented 3 years ago

While using alignment mode using hg19, I am getting following error.

08:42:02.883 [main] INFO java.lang.Class - To run: /home/ubuntu/COMPSRA/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /home/ubuntu/COMPSRA/bundle_v1/db/star/hg19 --genomeFastaFiles /home/ubuntu/COMPSRA/bundle_v1/db/star/hg19/hg19.fa.gz Dec 08 08:42:02 ..... started STAR run Dec 08 08:42:02 ... starting to generate Genome files

EXITING because of INPUT ERROR: the file format of the genomeFastaFile: /home/ubuntu/COMPSRA/bundle_v1/db/star/hg19/hg19.fa.gz is not fasta: the first character is '' (31), not '>'. Solution: check formatting of the fasta file. Make sure the file is uncompressed (unzipped).

Dec 08 08:42:02 ...... FATAL ERROR, exiting 08:42:02.904 [pool-2-thread-1] INFO java.lang.Class - To run: /home/ubuntu/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 /home/ubuntu/bundle_v1/db/star/hg19 --readFilesIn /home/smallrnaseq/raw/An_T_R1/An_T_R1_17to51_FitRead.fastq.gz --outFileNamePrefix /home/smallrnaseq/raw/An_T_R1/An_T_R1_17to51_FitReadSTAR

EXITING because of FATAL ERROR: could not create output file: /home/smallrnaseq/raw/An_T_R1/An_T_R1_17to51_FitRead_STAR_Log.out Check if the path /home/smallrnaseq/raw/An_T_R1/An_T_R1_17to51_FitReadSTAR exists and you have permissions to write there

Dec 08 08:42:02 ...... FATAL ERROR, exiting 08:42:02.908 [pool-2-thread-1] ERROR edu.harvard.channing.compass.core.Factory - /home/smallrnaseq/raw/An_T_R1/An_T_R1_17to51_FitRead_AlnReport.txt (No such file or directory) 08:42:02.909 [main] INFO edu.harvard.channing.compass.core.aln.Alignment - java.lang.NullPointerException 08:42:02.909 [main] INFO edu.harvard.channing.compass.core.Produce - Error: Alignment module fails!

cougarlj commented 3 years ago

Please try to use gunzip command to un-compress the file hg19.fa.gz. I guess STAR can only accept hg19.fa file.

drumair commented 3 years ago

I tried using gunzip, and deleted the hg19.fa.gz file, but it searches for the same, whereas when I use hg38 ref, it directly uses hg38.fa

10:09:05.039 [main] INFO java.lang.Class - To run: /apps/comsra/COMPSRA-master/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /opt/apps/comsra/COMPSRA-master/bundle_v1/db/star/hg38 --genomeFastaFiles /opt/apps/comsra/COMPSRA-master/bundle_v1/db/star/hg38/hg38.fa

cougarlj commented 3 years ago

There may be a bug for hg19. So, anyway, you can directly run STAR using the command, but not through COMPSRA for this step. Please directly run the command (/home/ubuntu/COMPSRA/bundle_v1/plug/star/STAR-2.5.3a/bin/Linux_x86_64/STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /home/ubuntu/COMPSRA/bundle_v1/db/star/hg19 --genomeFastaFiles /home/ubuntu/COMPSRA/bundle_v1/db/star/hg19/hg19.fa)

If it doesn't work, please let me know.

drumair commented 3 years ago

It works, thanks.