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Problem with Saminfo files

I have 2 questions.

  1. I am working on RNA-seq data and using Hisat. I am submitting it as job. my script is hisat2 -p 55 -x <htidex files> -q (to recognize fastq) -1 <file1_pairedend> -2 <file2_pairedend> -S /path/xyz.sam &> /path/xyz.sam.info (I worked with the same command but never had problem) I am getting sam files but my sam.info file has 0 kb.
  2. Also, after using SAMTOOLcommand: samtools view -bS test.sam > test.bam I am getting error message "SAM header is present: 194 sequences. Parse error at line 39349126: missing colon in auxiliary data Aborted". What could be the cause for both the issues.Can somebody help please. Thanks
rna-seq
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written by chowdhury • chowdhury

2 answers

  1. 2> /path/xyz.sam.info, not &> /path/xyz.sam.info
  2. Post line 39349126. As indicated in the error, it's presumably missing a colon in an auxiliary tag.
• 0 views • link
written by Devon Ryan Devon Ryan

2>, not &>

I don't think that's the problem. 2> redirects standard error and &> redirects standard error and standard output.

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written by novice novice

Thank You for the reply. I have a question.I have fixed the sam parsing error. The size is around 55 gb for sam files and 6gb for sorted bam files.I have submitted sam to direct bam conversion as a job and in the error file, I am getting the following message: "SAM Tools version 0.1.18 loaded. [samopen] SAM header is present: 194 sequences. [bam_sort_core] merging from 87 files...". Is this normal to have such efiles?

Thanks

• 0 views • link
written by chowdhury • chowdhury

Yes it is normal to have the BAM file be much smaller since it is binary and compressed.

Note: Please move this command against @Devon's by using the ADD COMMENT button. This helps keep the threads logically organized.

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written by GenoMax GenoMax

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