Error running SOAPIndel

[Lisle Mose]

Hello,

We are running sporadic errors running SOAPIndel where no results are produced.

Looking in the log directory, we see messages similar to the following for each chromosome:

[lmose@hm1 soap_indel]$ cat log/01_cr_1:1-249250621.log

[31 14:32:22] Reading the insert_size and RG information

[31 14:32:22] Reading the reference sequence

[31 14:32:28] Start reading region(1:1-249250621) from mappings(/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO)

[bam_header_read] EOF marker is absent. The input is probably truncated.

[31 14:39:33] 100.00%

Unfinished region(1:1-249250621) from mappings(/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/soapIndel.mapping.list.AUTO)

The BAM files being processed work fine with samtools, freebayes, pindel, GATK, etc.  For example:

samtools flagstat normal.bam

122208970 + 0 in total (QC-passed reads + QC-failed reads)

36261987 + 0 duplicates

119973698 + 0 mapped (98.17%:nan%)

122208970 + 0 paired in sequencing

61104485 + 0 read1

61104485 + 0 read2

118806244 + 0 properly paired (97.22%:nan%)

119562314 + 0 with itself and mate mapped

411384 + 0 singletons (0.34%:nan%)

353626 + 0 with mate mapped to a different chr

274412 + 0 with mate mapped to a different chr (mapQ>=5)

Any ideas as to what might cause this error?

Thanks!