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MapSplice2 gives error if the thread count (-p value) is greater than 2 mali_s Bioinformatics 0 07-22-2021 03:38 AM
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Old 07-22-2021, 04:12 AM   #1
mali_s
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Location: India

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Default MapSplice2 gives error if the thread count (-p value) is greater than 2

Hello! I get a multi-threading error while using MapSplice2. All the reference fasta files and index files were generated accordingly, as mentioned in the website. (http://www.netlab.uky.edu/p/bioinfo/MapSplice2UserGuide)

I get an error after it evaluates given files/parameters but before starting Mapsplice-multithread when the thread count was -p55. Then I made it run by default which is -p 1. It was working. It also works for -p 2. More than 2 it does not work

But I want to run it on more number of threads for parallel aligning as it's taking so much time for default setting. Please help me out with this.


Quote:
python2 software/MapSplice2/mapsplice.py -1 reads/file_1_trim.fastq -2 reads/file_2_trim.fastq --fusion -c mapsplice_fasta_files/ -x index_files/index -p 55 -o masplice_out

-----------------------------------------------
[Thu Jul 22 17:53:58 2021] Beginning Mapsplice run (MapSplice v2.2.1)
[Thu Jul 22 17:53:58 2021] Bin directory: software/MapSplice2/bin/
[Thu Jul 22 17:53:58 2021] Preparing output location masplice_out/
[Thu Jul 22 17:53:58 2021] Checking files or directory: reads/file_1_trim.fastq
[Thu Jul 22 17:53:58 2021] Checking files or directory: reads/file_2_trim.fastq
[Thu Jul 22 17:53:58 2021] Checking files or directory: mapsplice_fasta_files//
[Thu Jul 22 17:53:58 2021] Checking Bowtie index files
[Thu Jul 22 17:53:58 2021] Inspecting Bowtie index files
[Thu Jul 22 17:53:58 2021] Checking reference sequence length
[Thu Jul 22 17:53:58 2021] Checking consistency of Bowtie index and reference sequence
[Thu Jul 22 17:53:58 2021] Checking read format
-----[Read Format: FASTQ]
-----[Read Type: Pair End]
-----[Total # Reads: 31643736]
-----[Max Read Length: 101]
-----[Min Read Length: 31]
-----[Max Quality Score: 74]
-----[Min Quality Score: 35]
-----[Quality Score Scale: Phred+33]
[Thu Jul 22 17:54:14 2021] Running MapSplice multi-thread
[MapSplice Running Failed]
Error: Running MapSplice multi-thread failed: -11

Last edited by mali_s; 07-29-2021 at 01:33 AM.
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Old 07-23-2021, 05:34 PM   #2
jahaltom
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Location: Ames, Iowa

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Hi mali_s,

How many cores are you using? How much memory do you have access to?
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Old 07-25-2021, 10:12 PM   #3
mali_s
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Hi jahaltom,

I have run it on a server having 112 cores with Centos 7 OS installed on it. And the memory I have access to is around 438G.
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