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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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[bam_sort_core] truncated file. Aborting. Fatal error_Segmentation Fault #185

Closed Guokun2019 closed 5 years ago

Guokun2019 commented 5 years ago

Hi there, Am now trying Breseq on mutation call for resequenced genome. After fixing several error, I got stucked here as shown below.

Info. on the packages I used: R version: 3.5.2 (2018-12-20) -- "Eggshell Igloo" bowtie2 --version: /home/ymer/anaconda3/bin/bowtie2-align-s version 2.3.4.3 64-bit samtools --version samtools 1.9 Breseq version: /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq --version: breseq 0.33.2

ALIGNED READ:12800000

Summary... Aligned reads: 12878240 Read alignments: 28029069 Alignments split on indels: 103513 Reads with alignments split on indels: 37876 Split alignments: 3553042 Reads with split alignments: 231231 +++ NOW PROCESSING Preliminary analysis of coverage distribution [samtools] import ./data/reference.fasta.fai ./03_candidate_junctions/best.sam ./03_candidate_junctions/best.unsorted.bam [samtools] sort --threads 4 -o ./03_candidate_junctions/best.bam -T ./03_candidate_junctions/best.bam ./03_candidate_junctions/best.unsorted.bam [bam_sort_core] truncated file. Aborting. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Segmentation Fault !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 10 stack frames. /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x43b436] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x43b6d5] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20) [0x7f11bcc68f20] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x65f448] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x65fbb1] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x5fe753] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x42e988] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x40a31e] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f11bcc4bb97] /home/ymer/Documents/breseq-0.33.2-Linux-x86_64/bin/breseq() [0x417ab9] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

I ran the analysis with ubuntu in a hard drive with 700 Gb available space. Hope to get a solution to this error. Best, Guokun

jeffreybarrick commented 5 years ago

Did you try deleting the entire output directory so that it runs in a clean environment? It seems like the run may have been previously interrupted and generated a bad intermediate file.

Guokun2019 commented 5 years ago

I ran the analysis on the desktop and deleted the previously generated folders before the run. Will try to run in a clean folder and see if it helps. Thanks. Guokun

Guokun2019 commented 5 years ago

Hi Jeff, Things did not get better on the run in with a clean output folder. Similar error occurred.

Summary... Aligned reads: 12878240 Read alignments: 28029069 Alignments split on indels: 103513 Reads with alignments split on indels: 37876 Split alignments: 3553042 Reads with split alignments: 231231 +++ NOW PROCESSING Preliminary analysis of coverage distribution [samtools] import STS25_20190124_OUTPUT/data/reference.fasta.fai STS25_20190124_OUTPUT/03_candidate_junctions/best.sam STS25_20190124_OUTPUT/03_candidate_junctions/best.unsorted.bam [samtools] sort --threads 4 -o STS25_20190124_OUTPUT/03_candidate_junctions/best.bam -T STS25_20190124_OUTPUT/03_candidate_junctions/best.bam STS25_20190124_OUTPUT/03_candidate_junctions/best.unsorted.bam [bam_sort_core] truncated file. Aborting. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Segmentation Fault !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 10 stack frames. Killed

Any additional tips? Thanks. Guokun

jeffreybarrick commented 5 years ago

Are you able to share the input files so that I can investigate the problem? (Email me at the address in the breseq header and I can provide a shared upload folder.)

On Jan 25, 2019, at 1:45 AM, Guokun2019 notifications@github.com wrote:

Hi Jeff, Things did not get better on the run in with a clean output folder. Similar error occurred.

Summary... Aligned reads: 12878240 Read alignments: 28029069 Alignments split on indels: 103513 Reads with alignments split on indels: 37876 Split alignments: 3553042 Reads with split alignments: 231231 +++ NOW PROCESSING Preliminary analysis of coverage distribution [samtools] import STS25_20190124_OUTPUT/data/reference.fasta.fai STS25_20190124_OUTPUT/03_candidate_junctions/best.sam STS25_20190124_OUTPUT/03_candidate_junctions/best.unsorted.bam [samtools] sort --threads 4 -o STS25_20190124_OUTPUT/03_candidate_junctions/best.bam -T STS25_20190124_OUTPUT/03_candidate_junctions/best.bam STS25_20190124_OUTPUT/03_candidate_junctions/best.unsorted.bam [bam_sort_core] truncated file. Aborting. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Segmentation Fault !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 10 stack frames. Killed

Any additional tips? Thanks. Guokun

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Guokun2019 commented 5 years ago

Thanks Jeff, Problem seems to be solved. What I changed is placing all files and breseq in a folder under home directory. Then with the debug on space issue with R, I got the output files finally. Hope these info. helps others as well. Best, Guokun