Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • GenoMax
    replied
    Originally posted by lupid View Post
    Hi to all of you again, I get my first the novo transcriptome, done the last week, but when I try to do the RSEM, it fail and say Do you know what to do?
    Create a new thread for this since the question is no longer related to the original thread (if the following does not fix the problem).

    Your files are in fastq format correct? I would advise changing the "-" character file names to something else. That is likely to get you into trouble with programs, in case they do not parse the names correctly.

    Leave a comment:


  • lupid
    replied
    Hi to all of you again, I get my first the novo transcriptome, done the last week, but when I try to do the RSEM, it fail and say
    CMD: set -o pipefail && bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/cmeneses/tomas/carpa/trinity_out.Trinity.fasta.bowtie -1 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R1_001r_-N_-a_-q20_-150.fastq -2 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R2_001r_-N_-a_-q20_-150.fastq | samtools view -F 4 -S -b -o PIr.bowtie.bam -
    Too few quality values for read: M01447:54:000000000-A8564:1:1113:13048:8317 1:N:0:2
    are you sure this is a FASTQ-int file?
    terminate called after throwing an instance of 'int'
    bash: line 1: 50810 Aborted (core dumped) bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/cmeneses/tomas/carpa/trinity_out.Trinity.fasta.bowtie -1 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R1_001r_-N_-a_-q20_-150.fastq -2 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R2_001r_-N_-a_-q20_-150.fastq
    50811 Done | samtools view -F 4 -S -b -o PIr.bowtie.bam -
    Do you know what to do?

    Leave a comment:


  • lupid
    replied
    You are great
    Code:
    ##### Done Running Trinity #####

    Leave a comment:


  • GenoMax
    replied
    Add execute permissions as above.

    Code:
    $ chmod a+x /trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl

    Leave a comment:


  • lupid
    replied
    now almost done but at the end show this
    Code:
    /trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl: Permiso denegado
    Trinity run failed. Must investigate error above.

    Leave a comment:


  • GenoMax
    replied
    Find out where trinity is located (likely under trinityrnaseq-2.0.x/Trinity). Replace with a real path (path_to below).
    Code:
    $ chmod a+x /path_to/Trinity

    Leave a comment:


  • lupid
    replied
    and how do I do that?

    Leave a comment:


  • GenoMax
    replied
    Looks like you need to add execute permissions for trinity.

    Leave a comment:


  • lupid
    replied
    I had to format my laptop, so I was reinstalling trinity, and get this error when run runMe.sh

    Code:
    tomas@PC:~/Documentos/rna-seq/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly$ ./runMe.sh 
    #!/bin/bash -ve
    
    
    if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
        gunzip -c reads.right.fq.gz > reads.right.fq
    fi
    
    if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
        gunzip -c reads.left.fq.gz > reads.left.fq
    fi
    
    if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
        gunzip -c reads2.right.fq.gz > reads2.right.fq
    fi
    
    if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
        gunzip -c reads2.left.fq.gz > reads2.left.fq
    fi
    
    
    
    #######################################################
    ##  Run Trinity to Generate Transcriptome Assemblies ##
    #######################################################
    
    ../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
    ./runMe.sh: línea 26: ../../Trinity: Permiso denegado

    Leave a comment:


  • lupid
    replied
    --verbose was the part of the command that I was looking for
    without this trinity don't start in my pc

    Leave a comment:


  • lupid
    replied
    And about my another question, what do you think?

    Leave a comment:


  • GenoMax
    replied
    Since you have 64G use a higher number (e.g. 16G) to see if you can get past the problem.

    Log the std out/err messages to a file (if you are not using a job scheduler) to see if you can catch additional details.

    Leave a comment:


  • lupid
    replied
    One question about trinity too, if I have two differents states of my samples, is better do trinity in both at the same time or I could do it in separate?

    Leave a comment:


  • lupid
    replied
    I read the same message
    My data are in average 8M reads

    Leave a comment:


  • GenoMax
    replied
    How big are you data files (# of reads)?

    This is a quote from Trinity site (and may have changed some but use this as a guide).

    Ideally, you will have access to a large-memory server, roughly having ~1G of RAM per 1M reads to be assembled.
    Your command line option (--max_memory 8G) may be limiting here.

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X