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Trying to create a .bam file without the need for a .sam file

Bioinformatics Asked on April 5, 2021

I’m trying to use the code specified in this link to create a .bam file without the need for a .sam file.

Here is the code I’m using:

bwa mem -R "@RGtID:$SAMPLEtPL:illuminatSM:$SAMPLE" 
    $REF_PATH/hg38.fasta 
    mapping/R1.fastq.gz 
    mapping/R2.fastq.gz | 
    samtools sort - | 
    tee mapping/$SAMPLE.bam | 
    samtools index - mapping/$SAMPLE.bam.bai 
    2>> log

and I get the following error:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
`[E::main_mem] fail to open file ` '.

The ref path and file locations work when creating and converting a .sam to a .bam file.
Any ideas?

2 Answers

This is an error from bwa saying that it can't find your input files:

Here's a checklist:

  1. Check that you have no whitespace after your newline breaks. I.e. is the very last character
  2. Check that you have no whitespace in any path names
  3. Quote your variables: $REF_PATH -> "$REF_PATH"
  4. Use set -x at the top of your bash script to debug.
  5. In general, read this

Correct answer by Bastian Schiffthaler on April 5, 2021

Why make this so complicated with the tee command?

I don't think you even can index an unsorted bam, so you have to wait until sorting is done before you index. Indexing is really short compared to mapping and sorting, you aren't saving much by trying to do both at once.

Answered by swbarnes2 on April 5, 2021

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