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Question: Subread alignment issue
0
Entering edit mode

Hi everyone,

I'm trying to map two fastq files to M. fascicularis genome using the following command:

./subread-align -t 0 --sortReadsByCoordinates -T 5 -i ../../subread_index_normal/Macaca_fascicularis_5.0_genome -r ../../../../disk1/goekberk/SRR_files/SRR7529837_2.fastq -o BAM_files/SRR7529837_2.bam

Yet I'm receiving the following error:

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      v1.6.4

//================================= setting ==================================\\
||                                                                            ||
|| Function      : Read alignment (RNA-Seq)                                   ||
|| Input file    : SRR7529837_2.fastq                                         ||
|| Output file   : SRR7529837_2.bam (BAM), Sorted                             ||
|| Index name    : Macaca_fascicularis_5.0_genome                             ||
||                                                                            ||
||                    ------------------------------------                    ||
||                                                                            ||
||                               Threads : 5                                  ||
||                          Phred offset : 33                                 ||
||                             Min votes : 3 / 10                             ||
||                        Max mismatches : 3                                  ||
||                      Max indel length : 5                                  ||
||            Report multi-mapping reads : no                                 ||
|| Max alignments per multi-mapping read : 1                                  ||
||                                                                            ||
\\============================================================================//

//================ Running (02-May-2019 16:13:20, pid=51088) =================\\
||                                                                            ||
|| The input file contains base space reads.                                  ||
|| The range of Phred scores observed in the data is [2,41]                   ||
*** Error in `./subread-align': malloc(): memory corruption: 0x0000000001f13390 ***
Aborted (core dumped)

I should also mention that each fastq file I'm dealing with is ~14 gb in size, so they are relatively large I guess. However, I'm not sure if the file size causes this error or is it something else. I tried to delete and re-download the fastq files in case they were corrupted, but received the same error.

I'd be more than happy if you could help me with this.

Best, Gökberk

ADD COMMENTlink 9 months ago gokberk • 30
Entering edit mode
0

How much memory is available on your machine? It is clearly a memory error:

Error in `./subread-align': malloc(): memory corruption: 0x0000000001f13390
ADD REPLYlink 9 months ago
ATpoint
17k
Entering edit mode
0

I guess I've more than 50 gb of memory on server, is it possible that it requires even more?

ADD REPLYlink 9 months ago
gokberk
• 30
Entering edit mode
0

What operating system are you on? Did you install from a precompiled binary matched to your OS, or from from source? Have you tried posting to the support site or user group linked from the subread home page? Those contacts might be best source of help for a malloc error like this one.

ADD REPLYlink 9 months ago
Ahill
♦ 1.5k
Entering edit mode
0
  • To check memory usage you can reanalyze and use the tools htop or glances to continually assess memory usage as the tool runs
  • My feeling is it might be a fragmented genome. If you do the following on the -FASTA sequence how many contigs does it report ?

samtools faidx ref.fasta

wc -l *.fai

ADD REPLYlink 9 months ago
colindaven
♦ 1.3k

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