MINION ERROR when running miRNA pipeline

Issue #102 resolved
Aviv created an issue

When I run miARma for miRNA analysis, I get the following error (look at the last two lines):

TERM environment variable not set. which: no minion in (/usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/bin:/apps/RH7U2/gnu/miRDeep/2.0.0.8/bin:/apps/RH7U2/intel/bowtie/1.1.2/bin:/apps/RH7U2/general/miRNA/1.7.2/:/home/labs/shlush/avivdm/perl5/bin:/apps/RH7U2/general/express/1.5.1/:/apps/RH7U2/gnu/mipgen/22-Dec-2016:/apps/RH7U2/gnu/mipgen/22-Dec-2016/tools:/apps/RH7U2/gnu/boost/1.62.0/bin:/apps/RH7U2/gnu/pindel/0.2.5b9/bin:/apps/RH7U2/gnu/star/2.5.3a/bin:/apps/RH7U2/general/bvatools/1.6//scripts/R:/apps/RH7U2/general/bvatools/1.6//scripts/perl:/apps/RH7U2/gnu/bamtools/2.4.1/bin:/apps/RH7U2/gnu/parallel/20170322/bin:/apps/RH7U2/general/IGV/2.3.88:/apps/RH7U2/intel/pear/0.9.10/bin:/apps/RH7U2/gnu/openmpi/2.0.1/bin:/apps/RH7U2/gnu/trinity/2.3.2//util:/apps/RH7U2/gnu/trinity/2.3.2/:/apps/RH7U2/gnu/ViennaRNA/2.3.1/bin:/apps/RH7U2/gnu/RNAz/2.1/bin:/apps/RH7U2/general/blast/2.2.26/bin:/apps/RH7U2/gnu/hmmer/3.1b2/bin:/apps/RH7U2/gnu/fastx/0.0.14/bin:/apps/RH7U2/gnu/tabix/0.2.6/bin:/apps/RH7U3/gnu/sra_sdk/2.3.5-2/bin64:/apps/RH7U2/gnu/kentUtils/bin:/apps/RH7U2/gnu/mysql/5.7.16/bin:/apps/RH7U2/gnu/cufflinks/2.2.1/bin:/apps/RH7U2//general/jre/8.111/bin:/apps/RH7U2//general/jdk/8.111/bin:/apps/RH7U2/gnu/clustalw/2.1/bin:/apps/RH7U2/general/fastqc/0.11.5/:/apps/RH7U2/gnu/perl/5.24.0/bin:/apps/RH7U2/gnu/rsem/1.3.0/bin:/apps/RH7U2/gnu/hisat/2.0.5/bin:/apps/RH7U2/gnu/tophat/2.1.1/bin:/apps/RH7U2/intel/bwa/0.7.15/bin:/apps/RH7U2/gnu/samtools/1.3.1/bin:/apps/RH7U2/intel/bedtools/2.26.0/scripts:/apps/RH7U2/intel/bedtools/2.26.0/genome:/apps/RH7U2/intel/bedtools/2.26.0/bin:/apps/RH7U2/intel/bowtie2/2.2.9/bin:/apps/RH7U2/intel/stringtie/1.3.3b/bin:/apps/RH7U2/gnu/fasta/36.3.8d/bin:/apps/RH7U2/gnu/fasta/36.3.8d/scripts:/apps/RH7U2/general/graphprot/1.1.3/:/apps/RH7U2/general/graphprot/1.1.3//bin:/apps/RH7U2/gnu/perf/5.12/bin:/apps/RH7U2/gnu/python/2.7.12/bin:/apps/RH7U2/gnu/libsvm/3.22/python:/apps/RH7U2/gnu/libsvm/3.22/tools:/apps/RH7U2/gnu/libsvm/3.22/bin:/apps/RH7U2/gnu/R/3.3.2/bin:/apps/RH7U2/gnu/rnashapes/2.1.6/bin:/usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/etc:/apps/RH7U2/general/IMOD/4.10.8/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/labs/shlush/avivdm/bin:/apps/RH7U2/general/miRNA/1.7.2/miARma/bin/common/fastqc/:/apps/RH7U2/general/miRNA/1.7.2/miARma/bin/Linux/kraken/) MINION ERROR :: system args failed: 256 : Is minion installed and exported to $PATH ? at /apps/RH7U2/general/miRNA/1.7.2/lib/CbBio/RNASeq/Adapt.pm line 1484.

Comments (10)

  1. Eduardo Andres Leon

    Dear Aviv, Thanks for using miARma. Could you check that the miARmaPath value in your ini file contains the value /apps/RH7U2/general/miRNA/1.7.2/miARma ? I guess this is the path where the binary is installed. In such a way, minion should be under /apps/RH7U2/general/miRNA/1.7.2/miARma/bin/Linux/kraken/minion

    Regards

  2. Aviv reporter

    <html style="direction: ltr;"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <style type="text/css">body p { margin-bottom: 0cm; margin-top: 0pt; } </style> </head> <body bidimailui-charset-is-forced="true" style="direction: ltr;" text="#000000" bgcolor="#FFFFFF"> Dear Eduardo,<br> <br> Many thanks for your prompt reply!<br> I will do as you stated.<br> Also, I would like to inquire if there is a way to skip the adapter removal step, since my fastq reads (for miRNA-seq) do not contain an adapter.<br> <br> Best wishes,<br> Aviv.<br> <br> <div class="moz-cite-prefix">On 29/01/18 09:43, Eduardo Andres Leon wrote:<br> </div> <blockquote type="cite"

  3. Eduardo Andres Leon

    Dear Aviv, I'm checking the code because I'm not sure if this is possible. I remember to include the adapter=No in the "Denovo" pipeline but as this is totally disadvised for known miRNA I'd like to check it twice. I'll let you know

  4. Aviv reporter

    <html style="direction: ltr;"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <style type="text/css">body p { margin-bottom: 0cm; margin-top: 0pt; } </style> </head> <body bidimailui-charset-is-forced="true" style="direction: ltr;" text="#000000" bgcolor="#FFFFFF"> Hi Eduardo,<br> <br> Thanks a lot!<br> I am looking forward to your answer.<br> <br> Aviv.<br> <br> <div class="moz-cite-prefix">On 29/01/18 10:13, Eduardo Andres Leon wrote:<br> </div> <blockquote type="cite"

  5. Eduardo Andres Leon

    Hi again, You only have to remove the [Adapter] section in your ini file (it can't be easier but this was introduced almost a year ago and I forgot about this). Once you run an ini file with no adapter you will see a message like the one with the arrow:

    #########################################################################   
    #   miARma, miRNA and RNASeq Multiprocess Analysis          #
    #                miARma v 1.7.2 (Dec-2017)                              #
    #                                                           #
    #   Created at Computational Biology and Bioinformatics Group (CbBio)   #
    #   Institute of Biomedicine of Seville. IBIS (Spain)                   #
    #   Copyright (c) 2017 IBIS. All rights reserved.                       #
    #   mail : miARma-devel@cbbio.es                                        #
    #########################################################################
    
    [Mon Jan 29 09:37:05 2018] Starting a miARma analysis for miRNA
    [Mon Jan 29 09:37:05 2018] Checking provided parameters for: Quality,Aligner,ReadCount,DEAnalysis,TargetPrediction. 
    [Mon Jan 29 09:37:05 2018] All parameters are correct.
    [Mon Jan 29 09:37:05 2018] Starting Quality Analysis.
    [Mon Jan 29 09:37:25 2018] Quality Analysis finished.
    ->[Mon Jan 29 09:37:25 2018] No processed files are found [neither cutadapt, nor reaper nor adaptrimming folders], assuming Examples/basic_examples/miRNAs/reads/ don't need to be proccessed
    [Mon Jan 29 09:37:25 2018] Starting a "Bowtie1" Alignment Analysis
    [Mon Jan 29 09:38:35 2018] "Bowtie1" Alignment Analysis finished
    [Mon Jan 29 09:38:35 2018] Starting a Readcount Analysis
    [Mon Jan 29 09:38:38 2018] Readcount Analysis finished.
    [Mon Jan 29 09:38:38 2018] Starting a differential expression analysis using EdgeR software(s)
    [Mon Jan 29 09:38:50 2018] Differential expression analysis finished.
    [Mon Jan 29 09:38:50 2018] Starting a target Prediction Analysis using miRGate
    [Mon Jan 29 09:40:58 2018] Target Prediction Analysis finished.
    [Mon Jan 29 09:40:58 2018] miARma finished. Job took 3 minutes
    
  6. Aviv reporter

    <html style="direction: ltr;"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <style type="text/css">body p { margin-bottom: 0cm; margin-top: 0pt; } </style> </head> <body bidimailui-charset-is-forced="true" style="direction: ltr;" text="#000000" bgcolor="#FFFFFF"> Thanks, Eduardo.<br> However, I tried this already, and it appears that Bowtie is looking for the cutadapt output, which, in this case, does not exist, and the run is aborted.<br> Could you please verify this on your end?<br> <br> Thanks,<br> Aviv.<br> <br> <div class="moz-cite-prefix">On 29/01/18 10:48, Eduardo Andres Leon wrote:<br> </div> <blockquote type="cite"

  7. Aviv reporter

    <html style="direction: ltr;"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <style type="text/css">body p { margin-bottom: 0cm; margin-top: 0pt; } </style> </head> <body bidimailui-charset-is-forced="true" style="direction: ltr;" text="#000000" bgcolor="#FFFFFF"> Hi Eduardo,<br> <br> I ran it again without the [Adapter] section and it seems to work just fine.<br> <br> Thanks a lot for your assistance,<br> Aviv.<br> <br> <div class="moz-cite-prefix">On 29/01/18 10:48, Eduardo Andres Leon wrote:<br> </div> <blockquote type="cite"

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