Popoolation2 mpileup2sync error

[rahulvrane]

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, < $ifh> line 2.
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Ý¿´ÄÛ(WÓúË:ðè8F ܹ£EOë>á¸KÝj¥O`îZã×£ÎØîÖq at /home/rahul/popoolation2/Modu les/Pileup.pm line 50, <$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!

[phdgrimm]

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.