error numpy

[berger juliette]

Hello everyone,

My assembly is currently running, but when I check the .log file, I see the same message repeated hundreds of times. Could you please tell me if this might affect the assembly? I am not using SuperTranscripts.

End of .log file: 

 --->

Trinity run failed. Must investigate error above.
warning, cmd: /home/genouest/cnrs_umr7618/jberger/Software/trinityrnaseq-v2.15.2/util/support_scripts/../../Trinity --single "/scratch/jberger/trinity_out_dir/read_partitions/Fb_0/CBin_463/c46328.trinity.reads.fa" --output "/scratch/jberger/trinity_out_dir/read_partitions/Fb_0/CBin_463/c46328.trinity.reads.fa.out" --CPU 1 --max_memory 1G --run_as_paired --seqType fa --trinity_complete --full_cleanup --no_salmon   failed with ret: 65280, going to retry.


Error encountered::  <!----
CMD: /home/genouest/cnrs_umr7618/jberger/Software/trinityrnaseq-v2.15.2/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py --trinity_fasta /scratch/jberger/trinity_out_dir/read_partitions/Fb_1/CBin_1900/c190101.trinity.reads.fa.out/Trinity.tmp.fasta --out_prefix /scratch/jberger/trinity_out_dir/read_partitions/Fb_1/CBin_1900/c190101.trinity.reads.fa.out/Trinity.tmp.fasta.ST --incl_cdna 2>tmp.985997.1776705259.stderr

Errmsg:
Traceback (most recent call last):
  File "/home/genouest/cnrs_umr7618/jberger/Software/trinityrnaseq-v2.15.2/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py", line 11, in <module>
    import numpy
ModuleNotFoundError: No module named 'numpy'



My script is realy simple:

#!/bin/bash
#SBATCH --job-nam=Trinity_Blasto
#SBATCH --output=Trinity_blasto.log
#SBATCH --ntasks=1
#SBATCH --error=Trinity_blasto.err
#SBATCH --mem=150G
#SBATCH --cpus-per-task=2

export PATH=/home/genouest/cnrs_umr7618/jberger/Software/jdk-17.0.10+7/bin:$PATH
export PATH=$HOME/local/bin:$PATH
/home/genouest/cnrs_umr7618/jberger/Software/trinityrnaseq-v2.15.2/Trinity \
  --seqType fq \
  --max_memory 150G \
  --samples_file sample.txt \
  --CPU 2

Best regards, 

Juliette

[Eduardo Almeida Costa]

It will depend a lot on how the Trinity  dependencies were installed, and also on the environment variables that were loaded, but a quick way (best case scenario) is to install numpy using the command "pip install numpy" or "pip3.xx install numpy", where "3.xx" is the version that is active in the environment (in some Linux distributions pip may or may not point to the most recently installed version).

My best regards.

Eduardo Almeida Costa

Analista Universitário - 73.528.957-1

CCAM/UESC

Tel: +55 73 3680 5212

-------------------------------------------------------------------------------------------------

“Considerando a legislação vigente sobre proteção de dados, em especial à Lei 13.709/2018 (Lei Geral de Proteção de Dados Pessoais), os signatários e destinatários deste e-mail se obrigam a manter o sigilo e a garantir a confidencialidade em relação aos dados pessoais a que tiverem acesso através da presente comunicação eletrônica.”

“Considering the current legislation on data protection, in particular Law 13.709/2018 (General Law for the Protection of Personal Data), the signatories and recipients of this e-mail must keep confidentiality and guarantee confidentiality in relation to the personal data to which they have access through this electronic communication.”

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/trinityrnaseq-users/c269b7c1-7ccf-49da-8520-dbbba21e2bfbn%40googlegroups.com.

[Tiago Hori]

You are missing the numpy module for Python. 

If you are on shared server, you are likely going to have to ask an admin to install. 

If you have installation privileges, you can install locally with the command pip install numpy 

The assembly is crashing at the read partition across gene “models”. It may not go further until that is solved. I am not sure. I haven’t used Trinity in a while.

T.

“I ain’t going to work for Maggie’s farm no more” 

“Some of those who work forces are the same that burn crosses” 

On Apr 20, 2026, at 7:22 PM, berger juliette <bergerju...@gmail.com> wrote:



--