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Truncated Bam error in recalibrated bam file
I am trying to complete my pipeline to get variant calls and annotation using various tools of gatk. I am getting stuck in last step of post-processing. Here is my post-processing steps:
- Sam-to-Bam Conversion
- Bam Validation
- Sort Bam file (by SORT_ORDER = "queryname")
- BAM fixmate
- Again sort Bam (by SORT_ORDER = "coordinate")
- Remove duplicates
- Indel realignment
Q1 : I am using the following command for sam-to-bam conversion:
samtools view -S [email protected] 30 -M -f 0x02 -b input_sam -o input_bam
where -f stands for considering only properly paired reads. I have checked that how many reads I have missed (means 0x04,0x08 etc). Very small amount of reads I have missed i.e. the size of original sam file is 26 gb and there is another sam with which has all the reads excluding 0x02 is 152 mb in size and . So it is ok to not to take all the reads other than properly paired because without -f, there are many error that stop the whole pipeline.
Q2 : Now up to indel realignment, everything goes fine. I am checking bam file in each stage with the help of samtools command :
samtools view -c outfile.bam and
samtools quickcheck -qv outfile.bam
Both shows the positive reports till indel realignment. But during BQSR, I am always getting the following error:
1. Following warning during covariates estimation:
WARN 04:28:08,395 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in,skipping dictionary validation
- Following error during applying BQSR:
# # A fatal error has been detected by the Java Runtime Environment: # # SIGSEGV (0xb) at pc=0x00007f2453644c7e, pid=41985, tid=0x00007f1c36250700 # # JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151 - 8u151- b12 -0ubuntu0.16.04.2-b12) # Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 ) # Problematic frame: # V [libjvm.so+0x61fc7e] # # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again #
When I checked the error report, then it shows the following message:
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007f0c1e489c7e, pid=15994, tid=0x00007f040204e700
# JRE version: OpenJDK Runtime Environment (8.0_151-b12) (build 1.8.0_151-8u151- b12-0ubuntu0.16.04.2-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.151-b12 mixed mode linux-amd64 )
# Problematic frame:
# V [libjvm.so+0x61fc7e]
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
# If you would like to submit a bug report, please visit:
--------------- T H R E A D ---------------
Current thread (0x00007f0c18029800): GCTaskThread [stack: 0x00007f0401f4e000,0x00007f040204f000] [id=16002]
siginfo: si_signo: 11 (SIGSEGV), si_code: 128 (SI_KERNEL), si_addr: 0x0000000000000000`
I can't show the complete error message because it is too long. But during starting, it never showed any error. When I experiment with
-nct, then this error starts coming even when I have removed all
-nct. Can you suggest me how to remove this error.