Header Leaderboard Ad

Collapse

MaSuRCa: Super reads failed - kUnitigLengths.txt is of size 0

Collapse

Announcement

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

  • MaSuRCa: Super reads failed - kUnitigLengths.txt is of size 0

    Hello,

    I am trying running an assembly with MaSuRCa but am getting an error at the step: "Computing super reads from PE".

    here's the output with the error:

    [[email protected] xxxx]$ cd Assembly_test/
    [[email protected] Assembly_test]$ ls
    assemble.sh guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 meanAndStdevByPrefix.pe.txt pe_data.tmp quorum_mer_db.jf work1
    environment.sh guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err
    ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352 masurca_jobscript.sh pe.cor.tmp.log quorum.err test_jobscript.sh
    [[email protected] Assembly_test]$ cat ESTIMATED_GENOME_SIZE.txt

    [[email protected] Assembly_test]$ cat masurca_assembly.o4302352
    ==============================================================
    job_number: 4302352
    exec_file: job_scripts/4302352
    submission_time: Thu Dec 9 09:07:38 2021
    owner: xxxx
    uid: xxxx
    group: xxxx
    gid: xxxx
    sge_o_home: /home/xxxx
    sge_o_log_name: xxxx
    sge_o_path: /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/lx-amd64:/opt/gridengine/bin/linux-x64/:/home/xxxx/bin
    sge_o_shell: /bin/bash
    sge_o_workdir: /cluster/project7/xxxx/Assembly_test
    sge_o_host: vic
    account: sge
    cwd: xxxx
    reserve: y
    hard resource_list: h_rt=1980000,h_vmem=16G,tmem=16G
    mail_options: abes
    mail_list: [email protected]
    notify: FALSE
    job_name: masurca_assembly
    jobshare: 0
    shell_list: NONE:/bin/bash
    env_list: TERM=NONE
    script_file: masurca_jobscript.sh
    parallel environment: smp range: 16
    project: external
    binding: NONE
    job_type: NONE
    usage 1: cpu=00:00:00, mem=0.00000 GB s, io=0.00000 GB, vmem=N/A, maxvmem=N/A
    binding 1: NONE
    scheduling info: (Collecting of scheduler job information is turned off)
    [Fri 10 Dec 18:31:14 GMT 2021] Processing pe library reads
    [Fri 10 Dec 18:58:34 GMT 2021] Average PE read length 250
    [Fri 10 Dec 18:58:34 GMT 2021] Using kmer size of 99 for the graph
    [Fri 10 Dec 18:58:35 GMT 2021] MIN_Q_CHAR: 33
    [Fri 10 Dec 18:58:35 GMT 2021] Creating mer database for Quorum
    [Fri 10 Dec 19:25:43 GMT 2021] Error correct PE
    [Sat 11 Dec 00:04:24 GMT 2021] Estimating genome size
    [Sat 11 Dec 00:04:24 GMT 2021] Estimated genome size:
    [Sat 11 Dec 00:04:24 GMT 2021] Creating k-unitigs with k=99
    [Sat 11 Dec 00:04:24 GMT 2021] Computing super reads from PE
    [Sat 11 Dec 00:04:24 GMT 2021] Super reads failed, check super1.err and files in ./work1/
    [xxxx]$

    so I had a look at the error file super1.err, here it is:

    [[email protected] xxxx]$ cat super1.err
    mkdir work1
    ufasta sizes -H /cluster/project7/Bovidae/Assembly_test/guillaumeKUnitigsAtLeast32bases_all.fasta > work1/kUnitigLengths.txt; wc -l work1/kUnitigLengths.txt | awk '{print $1}' > work1/numKUnitigs.txt; tail -n 1 work1/kUnitigLengths.txt | awk '{print $1+1}' > work1/maxKUnitigNumber.txt
    Error with file '/cluster/project7/Bovidae/Assembly_test/guillaumeKUnitigsAtLeast32bases_all.fasta'
    Output file "work1/kUnitigLengths.txt" is of size 0, must be at least of size 1. Bye!
    mv work1/numKUnitigs.txt work1/createLengthStatisticsFiles.Failed
    mv work1/maxKUnitigNumber.txt work1/createLengthStatisticsFiles.Failed
    mv work1/kUnitigLengths.txt work1/createLengthStatisticsFiles.Failed

    I had a look around but couldn't find a solution,

    help would be much appreciated!

    thank you
    S
    Last edited by Inexperienced_Researcher; 12-22-2021, 06:06 AM. Reason: typos

Latest Articles

Collapse

  • seqadmin
    Improved Targeted Sequencing: A Comprehensive Guide to Amplicon Sequencing
    by seqadmin



    Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...
    03-21-2023, 01:49 PM
  • seqadmin
    Targeted Sequencing: Choosing Between Hybridization Capture and Amplicon Sequencing
    by seqadmin




    Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...
    03-10-2023, 05:31 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-24-2023, 02:45 PM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2023, 12:26 PM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-17-2023, 12:32 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-15-2023, 12:42 PM
0 responses
23 views
0 likes
Last Post seqadmin  
Working...
X