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NGLess: NGS with less work
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ngless-1.3.0-bwa not found #147

Closed liuxianghui closed 3 years ago

liuxianghui commented 3 years ago

Dear Sir: I install new version 1.3 of ngless recently using conda ( in the past, I had the 1.1 version and I removed the old one) by creating a new env. However, when I tried to run this. I found this error. --- semes that ngless-1.3.0-bwa is not found?? What is wrong? Shall it be located at the same directory as ngless in conda which is /gpfs0/scratch/xianghui/software/anaconda3/envs/ngless/bin/? Xianghui

The following is from the log file of my job. /gpfs0/scratch/xianghui/software/anaconda3/envs/ngless/bin/ngless Exiting after fatal error while loading and running script System Error (NGLess was not able to access some necessary resource) ^[[31mCannot find ngless-1.3.0-bwa on the system and this is a build without embedded dependencies. ^[[0m NGLess v1.3.0 (C) NGLess authors https://ngless.embl.de/

When publishing results from this script, please cite the following references:

     - Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T., and Bork, P.,
     NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. in
     Microbiome 7:84 (2019). DOI: http://doi.org/10.1186/s40168-019-0684-8

     -

     - Li, H., 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv
     preprint arXiv:1303.3997.

     - MOCAT2: a metagenomic assembly, annotation and profiling framework. Kultima JR, Coelho LP, Forslund
     K, Huerta-Cepas J, Li S, Driessen M, et al. (2016) Bioinformatics (2016)
     doi:10.1093/bioinformatics/btw183

     - MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit. Kultima JR, Sunagawa S, Li J, Chen W, Chen
     H, Mende DR, et al. (2012) PLoS ONE 7(10): e47656. doi:10.1371/journal.pone.0047656

  ======================================================================================
 Resource Usage on 2021-07-09 17:53:18.966942:
 JobId: 116319.pbs01                                 Project: all
 Submission Host: ln-0001.scelse.sg
 Exit Status: 1
 NCPUs Requested: 48                                 NCPUs Used: 48
 Memory Requested: None                              Memory Used: 89760kb
 Vmem Used: 1074418764kb
 CPU Time Used: 00:27:52
 Walltime requested: None                    Walltime Used: 00:27:55
 Start Time: Fri Jul  9 17:25:21 2021
 End Time: Fri Jul  9 17:53:18 2021
 Execution Nodes Used: (ca-0012:ncpus=48)
 ======================================================================================

~

luispedro commented 3 years ago

This is strange. Can you try running:

ngless --verbose --check-install

I would expect the bwa to be at /gpfs0/scratch/xianghui/software/anaconda3/envs/ngless/share/ngless/bin/ngless-1.3.0-bwa. Is there nothing there?

liuxianghui commented 3 years ago

I found out bwa is there but it is not set with right of execution. Surprising!. After I chmod +x for it. Then ngless --verbose --check-install seems to be working fine.

On Sat, Jul 10, 2021 at 10:41 PM Luis Pedro Coelho @.***> wrote:

This is strange. Can you try running:

ngless --verbose --check-install

I would expect the bwa to be at /gpfs0/scratch/xianghui/software/anaconda3/envs/ngless/share/ngless/bin/ngless-1.3.0-bwa. Is there nothing there?

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luispedro commented 3 years ago

Thanks! I will make NGLess give more information for this case