BWA error mapping RNA-seq data to human reference

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Natasha Arora

Dec 2, 2020, 6:57:25 PM12/2/20
to NGLess
Dear ngless Team,
I have RNA-seq data from human body sites, and I would like to remove the human reads (keeping all microorganism sequences). Managed to install ngless on a macOS Big Sur after Luis pointed me out to the location for the file (, and after changing permissions to get it to run. The code I am running is very simple, and am doing so on a test fastq file containing only a small number of reads. Please note that in the code I had to specify I was using ngless 1.1 in order to get the reference hg19 to download (did not work if I specified I was using ngless 1.2 as it could not access the website to download it).

$ngless "1.1"

$input = fastq('test.fq')

$mapped_hg19 = map(input, reference='hg19')

The error I encounter is with bwa mem and I wonder if it has to do with not having paired end reads. Maybe I need to specify I have single read sequencing somewhere, but how? 

"Failed command

Executable used:: /Users/natashaarora/Documents/Programmes/NGLess-1/bin/../share/ngless/bin/ngless-1.2.0-bwa

Command line was::

mem -t 1 -K 100000000 /Users/natashaarora/Documents/Programmes/NGLess-1/bin/../share/ngless/data/References/hg19/Sequence/BWAIndex/reference.fa-bwa-0.7.17.gz -p -

Error code was 1.

Stdout: <captured by inner process>

Stderr: [M::bwa_idx_load_from_disk] read 0 ALT contigs

[E::main_mem] fail to open file `-p'."

I apologise in advance if I have missed something very basic. Thank you very much for your help.


Luis Pedro Coelho

Dec 5, 2020, 10:39:52 PM12/5/20
to NGLess List, shaojun pan
Dear Natasha,

Indeed, I don't see any reason why this should not work. In fact, it works for me (on Linux), as it should.

I CC Shaojun who did the MacOS X building. @Shaojun: can you test Natasha's issue on Mac and see if you see the same issue.


Luis Pedro Coelho | Fudan University |
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