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  • Popoolation2 mpileup2sync error

    Hello,

    I have been trying to convert a mpileup format file to a sync file for usage in the population genetics program Popoolation2. However whenever I attempt this, I get an error saying:
    [rahul@__folder]$ perl ~/popoolation2/mpileup2sync.pl --fastq-type sanger --input NEWsed-Ii.Is.mpileup --output NEWsed-Ii.Is.sync

    Use of uninitialized value $rc in uc at /home/rahul/popoolation2/Modules/Pileup. pm line 43, <$ifh> line 1.
    Argument "$^DM-^B^OM-X^$tM-:M-S" isn't numeric in numeric eq (==) at /home/rahul /popoolation2/Modules/Pileup.pm line 87, <$ifh> line 2.
    Argument "KM-|BM-^IM-XM-0M-lM-F^ZM-AU(_M-ybM-^Gf^ZM-^H^FM-^\M-^OXM-c..." isn't n umeric in numeric eq (==) at /home/rahul/popoolation2/Modules/Pileup.pm line 87, <$ifh> line 2.
    Argument "_M-yyM-hl^UM-JW?M-PM-,)M-VM-,p^'M-^G^U^M-c@3M-v-kM-$U&^_..." isn't num eric in numeric eq (==) at /home/rahul/popoolation2/Modules/Pileup.pm line 87, < $ifh> line 2.
    Argument "DM-^Y^\^POX/M-FM-^F)M-NM-KM-d\0xM-^]^N1M-RM-{rM-^A;%6GM-<..." isn't nu meric in numeric eq (==) at /home/rahul/popoolation2/Modules/Pileup.pm line 87, <$ifh> line 2.
    Argument "M-eM-H:bM-OfM-vM-HwM-NM-5M-XM-9fdM-^G^\7CT;_M-#M-^M-9M-...." isn't num eric in numeric eq (==) at /home/rahul/popoolation2/Modules/Pileup.pm line 87, < $ifh> line 2.
    ****ed entry b0M*()Jr@Ú|@¤1

    2D(.*Á~ñ ¢AÈSV.NÌ-ÉÏÏ)K-*Z`k*g¨gh¡*QdiadediªÉŦè9ÿBC2 µ}àfGqß 8tH $Ø^$tºÓ N5@Æ`ãfBHb'N0`Ó
    M5Í6`lÜè½÷Þ{oò̾Ý}»ï;o¿/:!tE¿Ùé³³ûfÙÛÛûà9¯Ùÿ<þãÐÞÝ÷öοì~ö
    ÜÃW,übÅPáß
    _9~#üØ»ì¢pÔÉÇÀ??TÂ]NùWjÇW|÷áõ«SðƦpb¥æp)áЫó+®ÂÉÃ}4ÂXã"âÙm®
    [Y7´ðo q~5¹ZAýH8{{óµra´zø¹èÀʪv}üz<gÐîáÕti6T°Ø¸Æ¿ODào_¾=Çßìpcð .6ØEµ¶¬¡Úü¾U®ìÈö+ûv©P*´3*
    ze£ßW
    ˶vMüNÕÉ=7@Àïv¬ìæAvßÛV¿¿ÕÑÖ,ìø9ØKCÛãü¨d¬Ì<
    ¬y¯}*Y G×ÊGêz~Ä:"ùø±a ò1åòpôòèRùjY"á5jy¥jc4Cg^ _ùyèlÊW?Ь)Ö¬p^'^ã@3ö-k¤U&·^ci¸¦J>¯ÙÁ2]ßÍäPß]ë@3®X
    xbª¹¬¯¿ý
    ¶×L£XØ·½f7Ü9âI\7*âþ*×t'¯ =×Áí¹nì
    åÈ:bÏfögï<ÏÜ®C3ñÄÍòÌiØcc?sîö£ë°GúĨuXO±±w=o{ëiì¯o½WhõÎß:â¶Ú·ß:µZ)wØÚzZí#[×=*sÛ
    èwnágí| :j DºÅ|Éú±wÇ*í±u§{ÜìÁEÛÛcã®ÃÅë;à
    Ý¿´ÄÛ(WÓúË:ðè8F ܹ£EOë>á¸KÝj¥O`îZã×£ÎØîÖq at /home/rahul/popoolation2/Modu les/Pileup.pm line 50, <$ifh> line 2.
    Or if I try the java version, I get:
    $ java -jar ~/popoolation2/mpileup2sync.jar --fastq-type sanger --input NEWsed-Ii.Is.mpileup --output NEW-Ii.Is.sync

    Exception in thread "main" java.lang.IllegalArgumentException: An error occured during parsing of the mpileup;
    Please make sure you are a.) using the correct encoding and b.) using the correc t mpileup format
    at BatchProcessor.processBatch(BatchProcessor.java:43)
    at Mpileup2SyncFramework.run(Mpileup2SyncFramework.java:55)
    at CommandLineParser.parseArguments(CommandLineParser.java:67)
    at Mpileup2syncMain.main(Mpileup2syncMain.java:17)
    I have verified the encoding of my files and have also fixed headers (for GATK). The data is from a HiSeq 2000 with Sanger Illumina1.9 encoding. Is there any way to fix this?

    Any help would be more than life saving!

  • #2
    I had this issue and was able to fix it by using a bam files that had been sorted and indexed in Samtools then run through Picard AddOrReplace prior to running the mpileup.

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