Step 1 Value Error

[harveyza]

Hey Alicia,

I'm trying to run nucleoATAC on ATAC-seq data from yeast, but am getting the following error in step 1:
nucleoatac run --bam in.bam --bed broadPeak.bed --fasta 288C.fa --out nucleo_out --cores 16

start run at: 2016-01-19 14:53
---------Step1: Computing Occupancy and Nucleosomal Insert Distribution---------
Traceback (most recent call last):
File "/home/zharvey/.local/bin/nucleoatac", line 31, in
nucleoatac_main(args)
File "/home/zharvey/.local/lib/python2.7/site-packages/nucleoatac/cli.py", line 56, in nucleoatac_main
run_occ(occ_args)
File "/home/zharvey/.local/lib/python2.7/site-packages/nucleoatac/run_occ.py", line 95, in run_occ
fragment_dist.getFragmentSizes(args.bam, chunks)
File "/home/zharvey/.local/lib/python2.7/site-packages/nucleoatac/Occupancy.py", line 28, in getFragmentSizes
self.fragmentsizes.calculateSizes(bamfile, chunks = chunklist)
File "/home/zharvey/.local/lib/python2.7/site-packages/pyatac/fragmentsizes.py", line 26, in calculateSizes
sizes = getFragmentSizesFromChunkList(chunks, bamfile, self.lower, self.upper, atac = self.atac)
File "pyatac/fragments.pyx", line 130, in pyatac.fragments.getFragmentSizesFromChunkList (/home/zharvey/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:5040)
File "pysam/calignmentfile.pyx", line 874, in pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10986)
ValueError: fetch called on bamfile without index

I have Cython 0.23.4, numpy 1.10.4, scipy 0.16.1, and pysam 0.8.4 and am running on a Red Hat distribution of Linux.

Any thoughts? I checked to make sure that the reference fasta has the same nomenclature as the BAM and BED files.

Any help appreciated.

[AliciaSchep]

The bam file must be indexed. And the index file must be in same directory as bam file. I think making sure that is true should fix this issue as the error that is arising is "fetch called on bamfile without index"

[harveyza]

Thanks, that did the trick!