cleaned.fq.gz: command not found

[albustruong]

Hi,

I'm trying to test run mapping a paired-end read of 1 sample of mine to rsem-indexing reference (Please see photos for where I gather and prepare them for mapping.

I use this script:

!/bin/bash

rsem-calculate-expression \ --bowtie2 --bowtie2-path /usr/bin --phred33-quals \ --paired-end \ --p 6 --output-genome-bam \ --sort-bam-by-coordinates / sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz \ sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq.gz \ ref \ sub1-Ca13mCh-LGC9389_L1_paired_end_quals \ 2>&1 | tee sub1-Ca13mCh-LGC9389_L1_log.txt

Error report is: ./mapping_sample.sh: line 8: sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz: command not found

Please help me. Thanks.

[cndewey]

That error message suggests that "sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz" is at the beginning of a command line. If you look at the line above that filename, you'll see that you used a forward slash "/" instead of a backslash "\". You need to use a backslash instead for line continuation.

[albustruong]

Hi @cndewey ,

Thanks a lot for your help. I corrected the forward slash "/" to a backlash "\":

!/bin/bash

rsem-calculate-expression \ --bowtie2 --bowtie2-path /usr/bin --phred33-quals \ --paired-end \ --p 6 --output-genome-bam \ --sort-bam-by-coordinates \ sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz \ sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq.gz \ ref \ sub1-Ca13mCh-LGC9389_L1_paired_end_quals \ 2>&1 | tee sub1-Ca13mCh-LGC9389_L1_log.txt

and the error is gone. However, I got another error:

Unknown option: sort-bam-by-coordinates

What should I do?

[cndewey]

That error means you have given an option (sort-bam-by-coordinates) to rsem-calculate-expression that it does not recognize. Please give the manual a careful read. The correct option is "--sort-bam-by-coordinate".