[Samtools-help] Fwd: Picard MarkDuplicates PairInfoMap Error

[saad k. <sk...@gm...>]

Hi

The error in subject of this email has been discussed in the email before.
http://sourceforge.net/mailarchive/message.php?msg_id=29769281

But I have tried everything in the above post. It does not seems to solve
my problem.

I have a paired end read fastq file which I have aligned using bwa-mem
algorithm. The file seems to get stuck at the markduplicates step in picard
tools and throws the PairInfoMap  error for a read with null as a prefix.

  null:FCC1L1WACXX:2:1112:17105:14391#ACACGCGG


FCC1L1WACXX:2:1112:17105:14391#ACACGCGG 97      Gm01    7036    15      90M
    Gm02    44876031        0
CTCAGACTTATCAAGTTAATCCTTGTGGCGTCTACCCTGACTTATCTTCCTTCATTGGAAGTGGCGTCATCCAAATCTTCGTAGCCTGTA

 bbbeeeeegggggiihhhiiihiiigfhhhiiiiihiiidhhhfhhihihhhihhiiiihiegghihgggeeeeecddddcccacbbccc
 NM:i:0  AS:i:90 XS:i:80
FCC1L1WACXX:2:1112:17105:14391#ACACGCGG 145     Gm01    7389    24
 38M2I46M4S      Gm02    26650290        0
CCTGCACAACATATTCCAGACTACCACTATTCTTGTCATCTTTGTGTTACAAATGTCCTTTTTAATATGTTACATTCTTGTCGACTCACA

 BcbZ`_]UV^RZMH\H\H^VHVNG_VHV\a\Gihgca^^OGhgdgc^OOOIIOHH^H^YI_PIQQJQbSd`KfffbJ_HOJ_JcaS\J^Y
 NM:i:11 AS:i:31 XS:i:20


As was suggested in one of the post to use Fixmatepairinformation from
picard tools but it seems to be throwing this error


Exception in thread "main" net.sf.samtools.SAMFormatException: Error
parsing text SAM file. Zero-length read without FZ, CS or CQ tag; File
SortSam_HN025.sam; Line 412

Kindly suggest a workaround over this error.

regards
Saad