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huishenlab / biscuit

BISulfite-seq CUI Toolkit
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Error [M::bwa_idx_load_from_disk] read 0 ALT contigs #11

Closed hariiyer16 closed 3 years ago

hariiyer16 commented 3 years ago

I get the following error while running a standard alignment . Error [M::bwa_idx_load_from_disk] read 0 ALT contigs

It will be great if I can get some help to see what's wrong. I can send the raw files if required.

Following are the details.

Version details: Program: BISCUIT (BISulfite-seq CUI Toolkit) Version: 0.3.16.20200420

  1. Reference genome: mm39; index was created using $biscuit index ~/RefGenome/mm39.fa Index looks fine with the following files (mm39.fa.bis.ann, mm39.fa.bis.amb, mm39.fa.par.bwt, mm39.fa.dau.bwt, mm39.fa.bis.pac, mm39.fa.par.sa, mm39.fa.dau.sa)
  2. Small dataset to run on (make sure the dataset returns the same error) I ca provide this by email attachment. For the sake of speed, I am trying it on a subset data that was subsetted using seqtk.
  3. Command(s) run biscuit align ~/RefGenome/mm39.fa read_pair1.fa.gz read_pair2.fa.gz | samblaster | samtools sort -o output_pe.bam -O BAM -
  4. Error given samblaster: Version 0.1.26 samblaster: Inputting from stdin samblaster: Outputting to stdout [M::bwa_idx_load_from_disk] read 0 ALT contigs [fread] Bad address samblaster: Input file is empty. Exiting. samblaster: Premature exit (return code 1).

Expected behavior I expected an bam file with the alignments. The dataset is a published data and it works with Bismark.

Computer Resources

Additional context I am new to running biscuit and trying for first time.

Thank you.

hariiyer16 commented 3 years ago

Hi Jacob. Seems it was a memory issue. I increased available memory and that resolved. Was trying to align abut 1900 read pairs. Tried using 12G memory and it worked. Thanks.