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



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  • 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:

    [[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/

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

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