HOMER's map-star.pl script exits with fatal error

Question

[emblake]

I'm using the map-star.pl script from HOMER to batch map multiple PE fastq files using the STAR aligner, and I'm getting a fatal error that I can't resolve:

map-star.pl -p 72 -x /home/USER/u01/genomes/star-indexes/hg38-starIndex file1.r1,file1.r2 file2.r1,file2.r2 ...

Returns,

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory Oct 18 12:52:05 ...... FATAL ERROR, exiting

I've checked the file path, and I do, in fact, have the genome index files generated:

[USER@XXXXX hg38-starIndex]$ pwd
/home/USER/u01/genomes/star-indexes/hg38-starIndex
[USER@XXXXX hg38-starIndex]$ ls -l
total 29056988
1200 Oct 18 09:13 chrLength.txt
3123 Oct 18 09:13 chrNameLength.txt
1923 Oct 18 09:13 chrName.txt
2129 Oct 18 09:13 chrStart.txt
41854837 Oct 18 09:33 exonGeTrInfo.tab
16985258 Oct 18 09:33 exonInfo.tab
928822 Oct 18 09:33 geneInfo.tab
3208868819 Oct 18 09:35 Genome
702 Oct 18 09:12 genomeParameters.txt
24881828956 Oct 18 09:37 SA
1565873619 Oct 18 09:37 SAindex
10235563 Oct 18 09:33 sjdbInfo.txt
8020752 Oct 18 09:33 sjdbList.fromGTF.out.tab
8019182 Oct 18 09:33 sjdbList.out.tab
11688566 Oct 18 09:33 transcriptInfo.tab

And a memory check gives the following:

[USER@XXXXX hg38-starIndex]$ free -m
              total        used        free      shared  buff/cache   available
Mem:         128689        1563      125640          11        1485      126703
Swap:          4095           0        4095

Any suggestions?? Thank you!

Answer 1

[emblake]

Invoking the map-star.pl script generates a seemingly innocuous error message:

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

Oct 18 12:52:05 ...... FATAL ERROR, exiting

The --genomeLoad Remove option at line 90 of the script seems to trigger the string from STAR.

I was additionally receiving a samtools sort [bam_sort] error where the .bam and .bai files were not being generated. At a closer look, revising line 183 of the script corrected the error and produced the .bam and .bai files.

line 183: samtools sort -@ $numCPUs2 $file.unsorted.bam $ogFile;

revised line 183: samtools sort -@ $numCPUs2 $file.unsorted.bam -o $ogFile.bam;