Gatk Baserecalibrator Error

Question

[youngcsong]

So here's a problem that's having me rip my hair out for past couple of hours. I am trying to follow through some of the data pre-processing procedures as described by GATK's Best Practices page. So far, I got to the point where I ran IndelRealigner without a problem, and producing an output BAM file that is supposed to be used as input file for BaseRecalibrator. Now, here's where I am having a problem. I am going to copy/paste the error messages here, and hopefully someone could give me some ideas on how to diagnose this issue.

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.8-1-g932cd3a): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: SAM/BAM file /projects/seqdev/ysong_snp_indel/GATK_preproc_recalibrate/H0D21ADXX_1.linked.bam is malformed: Premature EOF.     Expected 352 but only received 306; BinaryCodec in readmode; file: /projects/seqdev/ysong_snp_indel/GATK_preproc_recalibrate/H0D21ADXX_1.linked.bam
##### ERROR ------------------------------------------------------------------------------------------

Funny thing is after I run this command, I get a 0 byte on the input BAM file, so I am forced to re-run IndelRealigner from the scratch (in fact, I have to go back and run this again). Do I have to use samtools view, and convert the BAM to SAM to see the format of the file itself?

Thanks in advance,

Young

[Dalia]

That's annoying that the input bam file gets set to 0...I'm pretty sure you are not doing this, but are you setting the output (-o) to the same file as the input in your command? very weird.

When you reran IndelRealigner did you get the same error again?

[youngcsong]

I am not setting the output as the same file as the input. Basically, I got tired of running around in circle, so I decided to make a copy of the IndelRealigner output as a backup, just in case things go unruly again. Just trying to do some things as described in the previous thread Error BAM file is malformed: Premature end of file using GATK tool BaseRecalibrator.

[youngcsong]

samtools view -c bam_file didn't produce any error and already tried converting bam to sam and checking the last couple lines...doesn't seem like there anything wrong at all with what the IndelRealigner produces.

[youngcsong]

okay...so I somehow got this thing to work...I had to go back to IndelRealigner and instead of of using -known, I used --knowAlleles. Not sure how this solves the problem, but things are back to normal again.