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  • yanzhangusa
    Junior Member
    • Jun 2009
    • 3
    #1

    help need for running Myrna

    I installed Myrna in our server and passed installation test. But when I try to run the example according to manual explained, I got the following error message for running yeast:
    yzhang@shadowfax:~/myrna-1.1.1/example/yeast> $MYRNA_HOME/myrna_local --input=$MYRNA_HOME/example/yeast/small.manifest --preprocess --reference=$MYRNA_REFS/yeast_ensembl_61 --output=output_small --quality solex
    a64 --cpus=5

    Myrna job
    ------------
    Local commands in: /tmp/myrna-IbVVLek3Z2/invoke.scripts/myrna.4200.sh
    Running...
    === Directory checker ===
    Time: 16:13:23 31-Mar-2011
    Input: /home/yzhang/myrna-1.1.1/example/yeast/small.manifest
    Output: /home/yzhang/myrna-1.1.1/example/yeast/output_small
    Intermediate: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200
    Counters: /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters
    Options: [ --force ]
    ==========================
    Stage 1 of 7. Preprocess
    ==========================
    Time: 16:13:23 31-Mar-2011
    === Map ===
    # parallel mappers: 5
    Input: /home/yzhang/myrna-1.1.1/example/yeast/small.manifest
    Output: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc
    Intermediate: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre
    Retries / delay: 3 / 5
    Options: [ --line-by-line --force ]
    Starting 5 mappers with command:
    perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt
    Pid 4286 processing input ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1 [1 of 2]...
    Pid 4287 processing input ftp://ftp-trace.ncbi.nih.gov/sra/sra...14339.lite.sra 0 rrp6_lsm1_pat1-1 [2 of 2]...
    Non-zero return (512) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
    Retrying in 5 seconds...
    Non-zero return (512) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04287 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04287'
    Retrying in 5 seconds...
    Non-zero return (2304) after closing pipe '| perl /home/yzhang/myrna-1.1.1/Copy.pl --compress=gzip --stop=0 --maxperfile 500000 --push /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc --counters /home/yzhang/myrna-1.1.1/example/yeast/output_small_counters/counters.txt >/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc/map-04286 2>/tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286'
    Retrying in 5 seconds...
    Fatal error 1.1.1:M130: Out of retries; aborting...

    When requesting support, please include the full output printed here.
    If a child process was the cause of the error, the output should
    include the relevant error message from the child's error log. You may
    be asked to provide additional files as well.
    Fatal error 1.1.1:M130: Out of retries; aborting...

    When requesting support, please include the full output printed here.
    If a child process was the cause of the error, the output should
    include the relevant error message from the child's error log. You may
    be asked to provide additional files as well.
    ******
    * Aborting master loop because child 4286 failed
    * (other children may also have failed)
    * Input file or string was:
    * ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1
    :
    * Error message is in file: /tmp/myrna-IbVVLek3Z2/myrna/intermediate/4200/preproc.map.pre/map.err/map-04286, also printed below
    ******
    * Copy.pl: Retrived 0 counters from previous stages
    * Copy.pl: Line: ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra 0 wild-1
    * Copy.pl: Not a comment line
    * Copy.pl: Doing unpaired entry SRR014335.lite.sra
    * Copy.pl: Fetching ftp://ftp-trace.ncbi.nih.gov/sra/sra...14335.lite.sra SRR014335.lite.sra 0
    * reporter:counter:Short read preprocessor,Read data fetched,510809892
    * sh: - : invalid option
    * Usage: sh [GNU long option] [option] ...
    * sh [GNU long option] [option] script-file ...
    * GNU long options:
    * --debug
    * --debugger
    * --dump-po-strings
    * --dump-strings
    * --help
    * --init-file
    * --login
    * --noediting
    * --noprofile
    * --norc
    * --posix
    * --protected
    * --rcfile
    * --restricted
    * --verbose
    * --version
    * --wordexp
    * Shell options:
    * -irsD or -c command or -O shopt_option (invocation only)
    * -abefhkmnptuvxBCHP or -o option
    * fastq-dump could not be found in SRATOOLKIT_HOME or PATH; please specify --sraconv
    ******
    Fatal error 1.1.1:M140: Aborting because child with PID 4286 exited abnormally

    When requesting support, please include the full output printed here.
    If a child process was the cause of the error, the output should
    include the relevant error message from the child's error log. You may
    be asked to provide additional files as well.
    Non-zero exitlevel from Preprocess stage
    yzhang@shadowfax:~/myrna-1.1.1/example/yeast>
    Tags: gene expression, myrna, rna-seq
  • George Wang
    Junior Member
    • Jul 2011
    • 2
    #2
    I am having same issue. Did you resolve the issue, and can you shed some lights? Thanks.

    Comment

    • yanzhangusa
      Junior Member
      • Jun 2009
      • 3
      #3
      use sratoolkit transfer sra format file to fastq format then run myrna. myran has problem running sratoolkit in its pipeline. I don't have any problem after that. you could download sratoolkit from NCBI. Good luck.

      Comment

      • George Wang
        Junior Member
        • Jul 2011
        • 2
        #4
        Great, Thank you very much!

        Comment

        • cutcopy11
          Member
          • Nov 2009
          • 19
          #5
          ~/Desktop/MYRNA_HOME/example/yeast$ ../../myrna_local --input=small.manifest --preprocess --reference=../../MYRNA_REFS/yeast_ensembl_61 --output=output_small --quality solexa64 --cpus=4

          I got the same error.

          If I physically download the files and convert them to fastq. How do I change the input option? --input=? Also, I no longer need the --preprocess option, right?
          Last edited by cutcopy11; 10-05-2011, 03:10 PM.

          Comment

          • yanzhangusa
            Junior Member
            • Jun 2009
            • 3
            #6
            still the same input just change filename list in small.manifest. don't need preprocess

            Comment

            • 9000revs
              Member
              • Jun 2013
              • 15
              #7
              Did you install the SRA toolkit and set the env var MYRNA_SRATOOLKIT_HOME?
              Last edited by 9000revs; 08-20-2013, 09:32 AM.

              Comment

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