Bowtie2 aligner error

Posted in General by Pratik Chandrani Fri May 27 2016 11:20:21 GMT+0000 (Coordinated Universal Time)·1·Viewed 1,588 times

I am running bowtie2 aligner imported from public apps to align RNAseq data (imported TCGA files) to indexed B37 (imported from common reference files) but again and again I am getting following error: Error This task ran into a problem during execution and did not finish. Command /opt/bowtie2-2.2.6/bowtie2 -p 8 -x GRCh37-lite_HPV_Redux --un 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.unpaired_unaligned.fastq.gz --al 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.unpaired_aligned.fastq.gz --un-conc 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.paired_unaligned.fastq.gz -a --rg-id id --rg PL:Illumina_HiSeq --rg SM:TCGA-CQ-6229-01A -1 /sbgenomics/Projects/5eeeb0e9-950d-42dc-9570-2eb54cee03a5/120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_1.fastq -2 /sbgenomics/Projects/5eeeb0e9-950d-42dc-9570-2eb54cee03a5/120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_2.fastq -S ./120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004.sam && mv 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.paired_unaligned.fastq.1.gz 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.paired_unaligned.1.fastq.gz && mv 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.paired_unaligned.fastq.2.gz 120815_UNC16-SN851_0177_BD13LJACXX_AGTTCC_L004_.paired_unaligned.2.fastq.gz failed with exit code 137. Can anybody suggest what is going wrong? I searched about error 137 but didn't find proper informaiton. Someone has suggested that 137 indicates that process is killed by some other process or by someone, but I don't understand why would that happen? Thanking you - Pratik
May 27, 2016

Hi Pratik,

I was able to run Bowtie on TCGA data against the GrCH37-lite-HPV_Redux public reference, so I'm not sure what's causing your current error. If you'd like to invite me (username: elehnert) to your project, I can try to identify what could be the issue.


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