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neufeld / pandaseq

PAired-eND Assembler for DNA sequences
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Pandaseq 2.0 - Mate-pairs do not match #26

Closed ajaymiyyapuram closed 10 years ago

ajaymiyyapuram commented 11 years ago

Hi,

Am using Pandaseq 2.0 on CentOS, I have generated the fastq files using Mothur. When I input the forward reads and reverse read files to PandaSeq, I get an following error -

ERR STOP Mate-pairs do not match: "7000004128189528:0:0:0:0:0:0:1:0:0:0" and "7000004128189528:0:0:0:0:0:0:1:0:0:0"

Could you enlighten me the cause for this issue. Below is the command I have run -

$pandaseq -f 5primerfiltered.fastq -r 3primerfiltered.fastq

Here is the sample data from my read files -

// 5primerfiltered.fastq

@7000004128189528:0:0:0:0:0:0:1:0:0:0 nCCTnCGGGnGnCnGCAGTGGGGAATATTGCGnAATGGGCGAAAGCCTGACGCAGCGACGCCGCGTGGnGGAAGAAGGCCTTCGGGTTnTAAnCCCCTTTCAGCAnGAACGAAGCGAAAGTnnCGGTACCTGnnGAAGAAGnACCGGCTAACTACGnGnnAGCAnCCGCnGTAATnCnTAGGGTGCAAGCGTTGTCCGGATTTACTnGGnGTAAAnAGCTCGTAGGCGGTCTGTCGCGTCGGATGTGAAAA +7000004128189528:0:0:0:0:0:0:1:0:0:0

AGF>AD??>?>A>A@D?DCC?BHHC?EDEG?>?GE@@CA?@DHEBBH@BB@?BC?CCBC?DCBBG?C>F@EAGHEH@DG@CFFEHHC>B?H>?CCAFFEGAACB>?DD?G@CBDFDH@CB>>@EDFDC@?F>>BHB@FBB>E?ADHCABG@F@AH>B>>C@?C>GB@?>BBH@F>?>H@?EF?FCAB@CFH@CDHF@DDDDGF@A>GD>?BAGA>FDCEADHCACCFEDBFH?A@CC@CBGHFAABH@DG

// 3primerfiltered.fastq

@7000004128189528:0:0:0:0:0:0:1:0:0:0 CCGGACTACCAnGGTATCnAnTCnTGTTCGCTCCnCACGCTTTCGCTnCTCAGCGTCnGTTGnGGCCCAGAGnCCCGCCTTCGnCACCGGTGTnCCTCnTGATATCTGCGCATTTCACCGCTACnCnAGGAATTnCAGnCTCCCnTGCCGCACTCTnGTnTGCCCGTATCGAATGCAGGCCCAGGGTTGAGCCCTGGGnTTTCACATCCGACGCGnCAGACCGCCTACGAGCTCTTTACGCCCAGTAAATCC +7000004128189528:0:0:0:0:0:0:1:0:0:0 DEFGEGAE@?E>DE@BDC>E>FF>@?FCAE?D@E>AGA?AAHB?HDE>@HC@DBDDE>CD@A>BB@EEGC@A>EDDAFGAAHH>ADE?HHB@C>AFD?>?EDAHDAG??BABB@DHDF?GAA@G>@>GAEH@?@>CBF>EHCFA>C@BBG@H@FDD>FA>BFCFC?HFFEDE@BCGCDDBHF?ABBCCDCGEEG?EBB>GE?HCCBA@BBCHHBE>?HEFFEBDGA?FHCE?DFHAHDAEB?H@FBAEE?BG

The same command and read files work well with PandaSeq 2.3 on Ubuntu OS.

Thanks, Ajay

apmasell commented 11 years ago
  1. PANDAseq 2.0 is quite old. If you are going to use CentOS, I recommend compiling the latest version from source.
  2. PANDAseq 2.3 is not the latest version for Ubuntu. What version of Ubuntu do you have? The packages should be automatically upgraded to the latest version if you are using Lucid, Precise, Quantal or Raring.
  3. These IDs are not typical output from CASAVA. How were they generated?
apmasell commented 10 years ago

Closing due to lack of response. If still interested, please reopen.