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

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


    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 guillaumeKUnitigsAtLeast32bases_all.fasta.tmp masurca_assembly.o4302352 pe_data.tmp quorum_mer_db.jf work1 guillaumeKUnitigsAtLeast32bases_all.jump.fasta masurca_config.txt pe.cor.fa pe.renamed.fastq super1.err
    ESTIMATED_GENOME_SIZE.txt masurca_assembly.e4302352 pe.cor.tmp.log quorum.err
    [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
    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/

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

Latest Articles


  • seqadmin
    Advanced Tools Transforming the Field of Cytogenomics
    by seqadmin

    At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...
    Today, 06:26 AM
  • seqadmin
    How RNA-Seq is Transforming Cancer Studies
    by seqadmin

    Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
    09-07-2023, 11:15 PM
  • seqadmin
    Methods for Investigating the Transcriptome
    by seqadmin

    Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.

    Whole Transcriptome RNA-seq
    Whole transcriptome sequencing...
    08-31-2023, 11:07 AM





Topics Statistics Last Post
Started by seqadmin, Today, 07:53 AM
0 responses
Last Post seqadmin  
Started by seqadmin, Yesterday, 07:42 AM
0 responses
Last Post seqadmin  
Started by seqadmin, 09-22-2023, 09:05 AM
0 responses
Last Post seqadmin  
Started by seqadmin, 09-21-2023, 06:18 AM
0 responses
Last Post seqadmin