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 if the p value is 2. Greater 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.
Also, it does work for another plant species. I get this error only for this species
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 if the p value is 2. Greater 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.
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[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/geno[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: -11me_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