I have always encountered such problem "This job was terminated because it used more memory than it was allocated." since last month， no matter how the input(fastq file) is large.
Here is the parameters I set for TopHat2:
|Is this library mate-paired?
|RNA-Seq FASTQ file
|13: Filter by quality on data 7 (22924873 reads)
|Use a built in reference genome or own from your history
|Select a reference genome
|TopHat settings to use
|Max realign edit distance
|Max edit distance
|Final read mismatches
|Use bowtie -n mode
|Anchor length (at least 3)
|Maximum number of mismatches that can appear in the anchor region of spliced alignment
|The minimum intron length
|The maximum intron length
|Allow indel search
|Max insertion length.
|Max deletion length.
|Maximum number of alignments to be allowed
|Minimum intron length that may be found during split-segment (default) search
|Maximum intron length that may be found during split-segment (default) search
|Number of mismatches allowed in each segment alignment for reads mapped independently
|Minimum length of read segments
|Use Own Junctions
|Use Gene Annotation Model
|Gene Model Annotations
|19: UCSC Main on Human: ensGene (genome)
|Use Raw Junctions
|Only look for supplied junctions
|Use Coverage Search
|Use Microexon Search
|Do Fusion Search
|Ignore some chromosomes such as chrM when detecting fusion break points
|Set Bowtie2 settings
|Specify read group?
|Job Resource Parameters
Does anyone know how to solve this problem? Thanks a lot!