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  • Viral Fusion Seq Error with the test data

    hi There,
    I am getting this error while running VFS (http://sourceforge.net/projects/viralfusionseq/) (VERSION: Revision 1250) on CentOS 5 release 5.10 (Final) system. After this error SSAKE also fails. Please let me know how this can be fixed. The portions of error output are below. Thanks for the help.

    Code:
    [COLOR="Teal"][B][SIZE="4"]Command[/SIZE][/B][/COLOR]
    perl 2.run.example.dataset.pl
    
    [FONT="Times New Roman"][B]The file "2.run.example.dataset.pl" has a the following command:[/B][/FONT]
    perl viral.fusion.pl --config vfs.conf --insertSIZE 350 HKCI5a CL7R_1_VFS.fq CL7R_2_VFS.fq
    
    [FONT="Times New Roman"][B]Both the fq files are included in vfs and I edited vfs.conf file to include the path of 3rd party software[/B].[/FONT]
    
    
    [COLOR="Teal"][B][SIZE="4"]Error 1[/SIZE][/B][/COLOR]
    Hashing CL7R_1_VFS.dynamic.min35.fq.gz
    Hashing CL7R_2_VFS.dynamic.min35.fq.gz
    Use of uninitialized value in concatenation (.) or string at
    	/data3/users/arun/Apps/vfs/include/RPmethod.pm line 268 (#1)
        (W uninitialized) An undefined value was used as if it were already
        defined.  It was interpreted as a "" or a 0, but maybe it was a mistake.
        To suppress this warning assign a defined value to your variables.
        
        To help you figure out what was undefined, perl tells you what operation
        you used the undefined value in.  Note, however, that perl optimizes your
        program and the operation displayed in the warning may not necessarily
        appear literally in your program.  For example, "that $foo" is
        usually optimized into "that " . $foo, and the warning will refer to
        the concatenation (.) operator, even though there is no . in your
        program.
        
    Hashing vfs_dev.HKCI5a.4h_map.fq
    Entering Essential::tx_targeted_assembly.
    Skipped Insert Size estimation. Supplied insert size: 350
    Essential::ssake_reads_prep
    Assuming fasta file
    Hashing vfs_dev.HKCI5a.RPm.out_2.fa
    Processing vfs_dev.HKCI5a.RPm.out_1.fa and vfs_dev.HKCI5a.RPm.out_2.fa
    Use of uninitialized value in pattern match (m//) at
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1236, <$Lfh> line 2 (#1)
    Use of uninitialized value in concatenation (.) or string at
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1238, <$Lfh> line 2 (#1)
    Use of uninitialized value in pattern match (m//) at
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1236, <$Lfh> line 4 (#1)
    Use of uninitialized value in concatenation (.) or string at
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1238, <$Lfh> line 4 (#1)
     
    
     --------------continued to even no of lines (6,8,10,12,14...36)--------------
    
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1236, <$Lfh> line 38 (#1)
    Use of uninitialized value in concatenation (.) or string at
    	/data3/users/arun/Apps/vfs/include/Essential.pm line 1238, <$Lfh> line 38 (#1)

    Code:
    [COLOR="Teal"][B][SIZE="4"]Error 2: SSAKE[/SIZE][/B][/COLOR]
    
    Running: /data3/users/arun/Apps/ssake_v3-8/SSAKE [v3.8]
    -f vfs_dev.HKCI5a.RPm.plus.vicinity.CS_FnR.ssake.in
    -s vfs_dev.HKCI5a.CSm.out.fullread.fa
    	-i 0
    -h 0
    -w 1
    -m 20
    -o 3
    -r 0.9
    -t 0
    -z 100
    -p 1
    -e 0.75
    -k 4
    -a 0.5
    -x 20
    Unpaired reads (optional) -g no-g
    Scaffolds: vfs_dev.HKCI5a.targeted.assembly.sensitive.scaffolds
    Merged contigs: vfs_dev.HKCI5a.targeted.assembly.sensitive.mergedcontigs
    Pairing issues: vfs_dev.HKCI5a.targeted.assembly.sensitive.pairing_issues
    Pairing distance distribution: vfs_dev.HKCI5a.targeted.assembly.sensitive.pairing_distribution.csv
    
    Contigs: vfs_dev.HKCI5a.targeted.assembly.sensitive.contigs
    Singlets: vfs_dev.HKCI5a.targeted.assembly.sensitive.singlets
    
    Excluded reads: vfs_dev.HKCI5a.targeted.assembly.sensitive.short
    Log: vfs_dev.HKCI5a.targeted.assembly.sensitive.log
    
    =>Reading sequences initiated Thu Jan  2 14:45:44 CST 2014
    Sequence reads loaded:
    616Input error at line #618: The sequence "0:" is not in the right format for paired-end reads  -- Fatal
    Make sure your input is in the form (input sequences can be of variable lengths):
    
    >test
    GCTACGACTATGACATACAGT:GTAGATTGATCGCATGCACGCT
    
    Where : separates paired reads.  Spaces, <<.>> or any characters other than A,C,G or T in your input file might have caused this error, including reads with Ns.
    mv: cannot stat `vfs_dev.HKCI5a_temp/*.targeted.*.contigs': No such file or directory
    Number of log files deleted:  0
    Last edited by akhattri; 01-06-2014, 02:59 PM.

  • #2
    I got also an error, cap3 crashed...

    hello,

    the run finished, but cap3 crahed twice...
    the CSm and .contigs-files are empty.

    what could be wrong with cap3?

    OS: Scientific Linux 6.3 (=RHEL 6.3), bwa 0.7.5a (problem?)



    Code:
    Executing:  /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a.CSm.out.MS.fa.sim -x cap3 >vfs_dev.HKCI5a.CSm.out.MS.fa.sim.cap3.log 2>>HKCI5a/cap3.log
    sh: line 1:  9066 Segmentation fault      (core dumped) /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a.CSm.out.MS.fa.sim -x cap3 > vfs_dev.HKCI5a.CSm.out.MS.fa.sim.cap3.log 2>> HKCI5a/cap3.log
    Entering Essential::create_simplified_readsID_fa.
    Entering Essential::cap3_run.
    Executing:  /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a.CSm.out.CS.fa.sim -x cap3 >vfs_dev.HKCI5a.CSm.out.CS.fa.sim.cap3.log 2>>HKCI5a/cap3.log
    sh: line 1:  9068 Segmentation fault      (core dumped) /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a.CSm.out.CS.fa.sim -x cap3 > vfs_dev.HKCI5a.CSm.out.CS.fa.sim.cap3.log 2>> HKCI5a/cap3.log

    Comment


    • #3
      Hi akhattri and dietmar13, I suppose there was some problem in processing the gzipped fastq files (that subsequently lead to the problem you see), I should have fixed the problem.

      Would you mind downloading the latest version again?



      Thanks.

      Marco
      Marco

      Comment


      • #4
        problem not solved

        dear marco,

        thank you, but the problem is the same.

        what could be wrong with cap3?
        file "vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim" is empty!

        cap3 works on their example data set xyz...

        OS: Scientific Linux 6.3 (=RHEL 6.3), bwa 0.7.5a (problem?)

        Code:
        Entering Essential::cap3_run.
        Executing:  /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a_gz.CSm.out.MS.fa.sim -x cap3 >vfs_dev.HKCI5a_gz.CSm.out.MS.fa.sim.cap3.log 2>>vfs_dev.HKCI5a_gz.log/cap3.log
        sh: line 1:  8445 Segmentation fault      (core dumped) /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a_gz.CSm.out.MS.fa.sim -x cap3 > vfs_dev.HKCI5a_gz.CSm.out.MS.fa.sim.cap3.log 2>> vfs_dev.HKCI5a_gz.log/cap3.log
        Entering Essential::create_simplified_readsID_fa.
        Entering Essential::cap3_run.
        Executing:  /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim -x cap3 >vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim.cap3.log 2>>vfs_dev.HKCI5a_gz.log/cap3.log
        sh: line 1:  8447 Segmentation fault      (core dumped) /home/ws/SW_install/CAP3/CAP3/cap3 vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim -x cap3 > vfs_dev.HKCI5a_gz.CSm.out.CS.fa.sim.cap3.log 2>> vfs_dev.HKCI5a_gz.log/cap3.log
        executing RPmethod::exec_RPmethod.
        Last edited by dietmar13; 01-06-2014, 03:24 AM.

        Comment

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