SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MapSplice2 gives error if the thread count (-p value) is greater than 2 mali_s Introductions 0 07-22-2021 02:31 AM
GATK::The contig index 20 is greater than the stored sequence count (1) Lessthan3 Bioinformatics 0 07-23-2012 11:54 AM
Help!Error: the contig index is greater then the stored sequence count HongxiangZheng Bioinformatics 3 05-14-2011 01:35 AM
tophat 1.2 multi thread mode error altodor Bioinformatics 2 02-16-2011 12:02 AM
tophat 1.2 multi thread mode error altodor RNA Sequencing 0 01-26-2011 12:04 PM

Reply
 
Thread Tools
Old 07-22-2021, 02:38 AM   #1
mali_s
Junior Member
 
Location: India

Join Date: Jul 2021
Posts: 4
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 12:36 AM.
mali_s is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO