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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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Output wihout .html files #333

Closed miniluphy closed 1 year ago

miniluphy commented 1 year ago

I got a litte confused by my output. The breseq (0.37.1-0) was successfully installed by the conda method according to the online documentation. However, when I followed the tutorial about clonal samples, something got wrong: breseq -l 60 -j 32 -o ZDB83_output -r REL606.gbk SRR098034.fastq

The output files did not include .html files as follows: image image

Your help will be much appreciated.

danieldeatherage commented 1 year ago

Thanks for reaching out. We're happy to help get this figured out.

It is also missing an output.done file which is generated when the final steps are completed successfully. Can you post the last few lines breseq generated on the command line?

miniluphy commented 1 year ago 
Error in bitmap(out_file, height = 6, width = 11, type = "png16m", res = 200,  :
  GhostScript was not found
In addition: Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/data/user/dingq/.conda/envs/breseq/lib64/R/modules//R_X11.so':
  libjpeg.so.8: cannot open shared object file: No such file or directory
Execution halted
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Error running command:
[system] R --vanilla < "/data/user/dingq/.conda/envs/breseq/bin/../share/breseq/plot_coverage.r" > "ZDB83_output/output/evidence/6282.r.log" --args in_file="ZDB83_outpu
t/output/evidence/6282_4.coverage.tab" out_file="ZDB83_output/output/evidence/REL606_1607940-1616705.png" pdf_output=0 total_only=0 window_start=1607940 window_end=1616
705 avg_coverage=0.0 fixed_coverage_scale=0
Result code: 256
FILE: libbreseq/common.h   LINE: 1411
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Backtrace with 12 stack frames.
breseq(+0x44cf4) [0x55a182083cf4]
breseq(+0xb98df) [0x55a1820f88df]
breseq(+0x177d09) [0x55a1821b6d09]
breseq(+0x13d1de) [0x55a18217c1de]
breseq(+0x13c839) [0x55a18217b839]
/lib64/libpthread.so.0(+0x620b) [0x2b586670c20b]
breseq(+0x13e442) [0x55a18217d442]
breseq(+0x13be11) [0x55a18217ae11]
breseq(+0x45f62) [0x55a182084f62]
/data/user/dingq/.conda/envs/breseq/bin/../lib/libstdc++.so.6(+0xcda93) [0x2b58665f5a93]
/lib64/libpthread.so.0(+0x7ea5) [0x2b586670dea5]
/lib64/libc.so.6(clone+0x6d) [0x2b5866d2296d]
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
terminate called without an active exception
/var/spool/slurm/d/job98969/slurm_script: line 10:  6282 Aborted                 breseq -l 60 -j 32 -o ZDB83_output -r REL606.gbk SRR098034.fastq

This is logfile.txt: slurm.txt Hope this helps. Thank you!

miniluphy commented 1 year ago

Update： The problem was probably generated by my linux server. I used conda to install ghostscript, and it works now. conda install -c conda-forge ghostscript The communication posted on “segmentation fault during candidate junctions phase” in those issues helped a lot. Thank you! Thank you very much for developing such a useful tool！