Problem aligning to nuclear genome

Hi Eliezer, could you check the thread below. The large memory error might be because the bed to bigwig converted is getting an empty file.
https://sourceforge.net/p/mitosalt/discussion/general/thread/0cd3fa85ad/?limit=25#b99c

If you run the pipeline with the delete temporary files option as "no", then one can check what each intermediate file generates. The order of the files would be:
1) tmp_$tag.bam: The alignment against Nuclear + Mitochondrial genome
3) tmp1_$tag.bam and tmp2_$tag.bam: Unmapped and Mt mapped reads extracted from the BAM above
4) tmp_final_$tag.bam: The unmapped and Mt mapped files merged
5) tmp_$tag.fq: The merged BAm above converted to FASTQ
6) tmp_$tag.maf: The FASTQ above aligned to Mt genome only using LAST
7) bam/$tag.bam: MAF output converted to BAM
8) tab/$tag.tab: MAF output converted to TSV
9) tmp_$tag.bg: BEDGRAPH output from bam/$tag.bam to visualize coverage If this file does not have any lines, the downstream bigwig conversion will fail with error needLargeMem
10) indel/$tag.cnmt.txt: Coverage estimate on the only Mt genome mapped reads
11) tmp_random_$tag.cov: Coverage of 1000 random regions on the nuclear genome If this file has not values then downstream mean nuclear coverage will fail with ERROR:Requested column 8...

For all the above, $tag is the study name to your run given for example:
perl MitoSAlt1.1.1.pl <config_file> <fastq file 1> <fastq file 2> <study name>

Please let us know if this helps.

-Regards
Swaraj

Hi Swaraj,
Thanks for your response, you are correct, the .bg file is empty, the .cov however is not, it has all the columns. In fact, I tried the solution you mention is the linked post for that prior to creating the ticket, but when I try this step:
groupBy -g 5 -c 8 -o mean -i random.cov
I get the same * ERROR: Requested column 8, but database file random.cov only has fields 1 - 0

In general, I don't understand why the bg file is empty to begin with, is it something on my system or with the sample or...?
Thanks,
Eliezer