GATK convert SAM to BAM

[cmccabe]

Following the GATK example but the spacing seems off in the command. Is it and how do I correct it? Thanks

java -jar picard.jar SortSam \ 
     INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \ 
     OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam  \ 
     SORT_ORDER=coordinate

[mastal]

the spacing looks OK to me.

[cmccabe]

Here is what it looks like in the ubuntu terminal:

cmccabe@DTV-A5211QLM:~$ java -jar picard.jar SortSam \ 
Error: Unable to access jarfile picard.jar
cmccabe@DTV-A5211QLM:~$      INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \ 
 : command not found
cmccabe@DTV-A5211QLM:~$      OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam  \ 
 : command not found
cmccabe@DTV-A5211QLM:~$      SORT_ORDER=coordinate
cmccabe@DTV-A5211QLM:~$ echo $PATH
/home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cmccabe/Desktop/NGS/bedtools2-25.0/bin:/home/cmccabe/Desktop/NGS/bbmap-35.59:/home/cmccabe/Desktop/NGS/FastQC-0.11.4:/home/cmccabe/Desktop/NGS/picard-tools-1.139

Thank you .

[blancha]

Just delete the extra white spaces.
You can use a text editor that displays white space to make your life easier.
I like TextWranger on Mac, which has the option to display white spaces.

java -jar picard.jar SortSam \
INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \
OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \
SORT_ORDER=coordinate

[cmccabe]

I use notepad++ with ubuntu and it is hard to see the spaces in yellow (not sure why this color was used). Thank you .