Seqanswers Leaderboard Ad

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:

    [xxxx@vic xxxx]$ cd Assembly_test/
    [xxxx@vic 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
    [xxxx@vic Assembly_test]$ cat ESTIMATED_GENOME_SIZE.txt

    [xxxx@vic 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:

    [xxxx@vic 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
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
31 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
40 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
205 views
0 likes
Last Post seqadmin  
Working...
X