shah-rohan/SmartMap

SmartMapPrep error message

Rjawabreh opened this issue · 2 comments

Rjawabreh commented

Hi, I'm trying to run SmartMapPrep before running SmartMap, and I got this error message
"sed: -e expression #1, char 0: no previous regular expression"
A splits directory was made but it was empty, same thing with the output SmartMapPrep output .bed.gz file.
This is the command I used:
$ SmartMapPrep -x GCA_000237925.5 -o SmartMapPrep_86_output -1 SRR6307186_1.fastq.gz -2 SRR6307186_2.fastq.gz

Rjawabreh commented

I tried to run it again and it seems the issue is with the Bowtie2 alignment, I get this error message:
"Error outputting data
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)"
I've already completed the alignment previously using the same required parameters used by SmartMapPrep, is there any way I can use my own .sam/.bam alignment file for this to evade the error?

mfper commented

Although this is probably too late to help the OP, I also found this error recently and managed to circumvent it.

The problem seems to be that the -s flag in SmartMapPrep which is described in the documentation as 'optional' and which has the objective of removing a prefix from the read names The bash script uses sed to remove the specified prefix and this throws an error if a prefix to be removed has not been specified using the -s flag.

I see two work arounds:

  1. Make sure to input some prefix for -s

  2. Modify the SmartMapPrep bash script to remove the sed function, if you don't want any prefix removed. Then it works.

  • 👍3