Getting unusual characters while generating output files in a bash script
Hi i im trying to run one command on mutliple files so i made a .sh script to do it:
bwa mem -M -R '@RG\tID:ERR040140\tLB:2517707\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR040140' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR040140_* > ERR040140.sam
bwa mem -M -R '@RG\tID:ERR046796\tLB:2799740\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR046796' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR046796_* > ERR046796.sam
bwa mem -M -R '@RG\tID:ERR046903\tLB:2806657\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR046903' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR046903_* > ERR046903.sam
bwa mem -M -R '@RG\tID:ERR067581\tLB:3712238\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067581' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067581_* > ERR067581.sam
bwa mem -M -R '@RG\tID:ERR067593\tLB:3712250\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067593' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067593_* > ERR067593.sam
bwa mem -M -R '@RG\tID:ERR067606\tLB:3712263\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067606' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067606_* > ERR067606.sam
bwa mem -M -R '@RG\tID:ERR067607\tLB:3712264\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067607' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067607_* > ERR067607.sam
bwa mem -M -R '@RG\tID:ERR067608\tLB:3712265\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067608' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067608_* > ERR067608.sam
bwa mem -M -R '@RG\tID:ERR067609\tLB:3712266\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067609' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067609_* > ERR067609.sam
bwa mem -M -R '@RG\tID:ERR067610\tLB:3712267\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067610' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067610_* > ERR067610.sam
bwa mem -M -R '@RG\tID:ERR067613\tLB:3712270\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067613' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067613_* > ERR067613.sam
bwa mem -M -R '@RG\tID:ERR067614\tLB:3712271\tPL:ILLUMINA\tPM:HiSeq2000\tSM:ERR067614' ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ERR067614_* > ERR067614.sam
But the output files are generating with unusual characters:
'ERR067610.sam'$'\r'
'ERR067614.sam'$'\r'
Whats the issue?
Can anyone help?
1 answer
The error was resolved using :
#dos2unix
sed `echo "s/\r//"` ../pre_xdr_20_batch_run.sh > pre_xdr_20_batch_run.sh
Secondly I found an answer to run it in a loop :
Log in to answer this question.
More posts like this
-
BWA align in human and parasite genome, and sort them
written by Bender •
-
Redirecting the output of a command related to another command
written by fra.r.silvestro •
-
Samtools equivalent of "CleanSam" Picard GATK?
written by Eliveri •
-
BWA aligner error: paired reads have different names
written by MAPK
-
How to pass arguments in a bash script to perform read alignment to the reference?
written by Karma
-
bwa mem: fail to locate the index files
written by little_more •
-
How to merge/combine multiple vcf from different samples to make one multi sample vcf file using GA…
written by S AR
-
there are not enough pairs message on screen when running BWA MEM
written by S AR
-
BWA mapping ERROR
written by meekadi •
-
Running BWA parallel on 1000 samples
written by ebrown1955
my guess: you're working with some windows files somewhere : https://en.wikipedia.org/wiki/Newline#Issues_with_different_newline_formats
see https://stackoverflow.com/questions/800030/remove-carriage-return-in-unix
Try
dos2unixon your script. It should remove windows line terminators.Unrelated: there must be a more efficient way (e.g. using a loop) to execute these commands, rather than listing them all separately in a bash script.
I agree - this looks like a job for
dos2unix, a very useful tool too have. The solutions found through Pierre's links are also plausible.\ris an end-line character. Another commonly-found one is^M.Yes there are first i'm trying to do this if i get success that i make a loop or something. And i ran :
It outputted:
But i found no change..
And if anyone suggest a better way of doing it like a loop that can get file name from a list?
The unique read group header (
stringafter-R) makes it a bit difficult for aforloop, unless you can extract thatstringeasily?The only thing that change in the read group header will be tID and tSM. that will be the file names.
Hello S AR ,
the similiar/same question you also asked on stackexchange. You should link to places where you asked the same question. Doing this everyone can see if your problem is maybe already solved.
Thanks.
fin swimmer