Hi
I ran bwa aln and it completed successfully. I have tried it numerous times and the same file sizes result so I assume this step is working correctly and the files are not truncated. However, when performing bwa sampe, I receive the following error:
I am not sure what file '1888]' refers to and I have tried numerous alignments and different versions of BWA to no avail. What might the problem be?
Thanks
Jom
I ran bwa aln and it completed successfully. I have tried it numerous times and the same file sizes result so I assume this step is working correctly and the files are not truncated. However, when performing bwa sampe, I receive the following error:
Code:
------------------------------------------------------------ # LSBATCH: User input source bwa-0.6.1; bwa sampe upregoakextractreal.fa LIB1167upregoakextract49.sai LIB1167upregoakextract49b.sai LIB1167_NoIndex_L005_R1.fastq LIB1167_NoIndex_L005_R2.fastq > L1167upregoakextract.sam ------------------------------------------------------------ Exited with exit code 134. Resource usage summary: CPU time : 0.19 sec. Max Memory : 2 MB Max Swap : 31 MB Max Processes : 1 Max Threads : 1 The output (if any) follows: [bns_restore_core] fail to open file '1888]'. Abort! /users/cd/jom/.lsbatch/1360003171.2694815: line 8: 28457 Aborted (core dumped) bwa sampe upregoakextractreal.fa LIB1167upregoakextract49.sai LIB1167upregoakextract49b.sai LIB1167_NoIndex_L005_R1.fastq LIB1167_NoIndex_L005_R2.fastq > L1167upregoakextract.sam "saisam1.out" 40011L, 2158332C
Thanks
Jom
Comment