Problem with the software Trinity

1

Hello, I am currently trying to assemble RNA-seq data with the software Trinity. I got an error related to samtools installation. Here is the script i use :
#!/bin/bash
#SBATCH --job-name trinity_dpla # this is a parameter to help you sort your job when listing it
#SBATCH --mem 100G
#SBATCH --cpus-per-task 12
#SBATCH --partition shared-cpu # the partition to use. By default debug-cpu
#SBATCH --time 12:00:00 # maximum run time.

ml GCC/8.3.0 SAMtools/1.10 OpenMPI/3.1.4 Trinity/2.9.1-Python-3.7.4

srun Trinity --seqType fq
–left “Rep1_1.sp.fastq.gz,Rep2_1.sp.fastq.gz”
–right “Rep1_2.sp.fastq.gz,Rep2_2.sp.fastq.gz”
–CPU 12
–max_memory 90G
–output /home/users/e/evann/scratch/01_Trinity_Assembly.

and here is the error i get

Trinity version: Trinity-v2.9.1
-ERROR: couldn’t run the network check to confirm latest Trinity software version.

Argument “error” isn’t numeric in numeric ne (!=) at /opt/ebsofts/Trinity/2.9.1-foss-2019b-Python-3.7.4/trinityrnaseq-v2.9.1/Trinity line 3865.
Error, need samtools installed that is at least as new as version 1.3 at /opt/ebsofts/Trinity/2.9.1-foss-2019b-Python-3.7.4/trinityrnaseq-v2.9.1/Trinity line 3866.
srun: error: cpu331: task 0: Exited with exit code 127

I didn’t find a solution to this. Can somebody help me?

Thank you in advance

2

Dear @Nathan.Evan

I’m compiling a recent version of Trinity as the one is using outdated dependencies. I’ll let you know once done, it takes some time because there is a lot of dependencies such as R.

3

Thank you very much @Yann.Sagon ^^

4

Dear @Yann.Sagon

I understand you probably have a lot to do, but we need this analysis relatively urgently. Do you have a time frame for when it will be ready ?

5

Hi, I had a couple of issue compiling this software as it has a bunch of dependencies and I was stuck when compiling the ~1300 extensions of R. Finally I found out that the compute node I was using to do the compilation wasn’t the one I expected (i.e. not the correct CPU, incompatible with some other nodes).

Well, ongoing process!

6

Okey, thank you very much and please tell me when I can run my analysis ^^

7

Please check: New software installed: Trinity version 2.15.2

8

Thank you so much ! Have a nice weekend