MapSplice2 gives error if the thread count (-p value) is greater than 2
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4 days ago
nkmalini97 • 0

Hello! I am using MapSplice2 to generate fusion candidates for Arabidopsis thaliana RNA-Seq data. 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.

Also, it does work for another plant species. I get this error only for this species. Please help me out with this

[sklab202@localhost ERR1876170]$ python2 /mnt/storage/sklab202/software/MapSplice2/mapsplice.py -1 reads/ERR1876170_1_trim.fastq -2 reads/ERR1876170_2_trim.fastq --fusion -c /mnt/storage/sklab202/genome_files/mapsplice_fasta_files/ -x /mnt/storage/sklab202/genome_files/index_files_mapsplice/at_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: /mnt/storage/sklab202/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/ERR1876170_1_trim.fastq [Thu Jul 22 17:53:58 2021] Checking files or directory: reads/ERR1876170_2_trim.fastq [Thu Jul 22 17:53:58 2021] Checking files or directory: /mnt/storage/sklab202/genome_files/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

Mapsplice2 fusion_candidates • 125 views
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Have you tried with an intermediate number of threads? (greater than 1 but lower than 55)

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Yeah. It was working for -p 1 and -p 2. More than two threads it gives that error

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