clemgoub/dnaPipeTE

Trinity iteration issues with Singularity container

heidihyang opened this issue · 4 comments

heidihyang commented

Hi Clement,

I successfully installed the Singularity container of dnaPipeTE on my cluster after having some issues with my previous installation, but I keep getting Trinity issues. In particular I'm getting this error:
awk: cannot open /global/scratch/users/heidihyang/001_tetragnathaTE/02_dnaPipeTE_outputs/test_001_output/Trinity_run0/chrysalis/readsToComponents.out.sort (No such file or directory) Must specify basic parameters: ex. Trinity --seqType fq --single reads.fq --max_memory 10G at /opt/dnaPipeTE/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 853. awk: cannot open /global/scratch/users/heidihyang/001_tetragnathaTE/02_dnaPipeTE_outputs/test_001_output/Trinity_run1/chrysalis/readsToComponents.out.sort (No such file or directory) Must specify basic parameters: ex. Trinity --seqType fq --single reads.fq --max_memory 10G at /opt/dnaPipeTE/bin/trinityrnaseq-Trinity-v2.5.1/Trinity line 853. sed: can't read /global/scratch/users/heidihyang/001_tetragnathaTE/02_dnaPipeTE_outputs/test_001_output/Trinity_run2/Trinity.fasta: No such file or directory awk: cannot open /global/scratch/users/heidihyang/001_tetragnathaTE/02_dnaPipeTE_outputs/test_001_output/Trinity_run2/Trinity.fasta (No such file or directory) /bin/sh: 1: -pa: not found

I've attached my log below.
001_test2_log.pdf

Also this is the command I ran: singularity exec /global/scratch/users/heidihyang/sing_DPTE/dnapipete.img python3 /opt/dnaPipeTE/dnaPipeTE.py -input /global/scratch/users/heidihyang/001_tetragnathaTE/01_data_from_jose/001_F.fastq.gz -output /global/scratch/users/heidihyang/001_tetragnathaTE/02_dnaPipeTE_outputs/test_001_output/ -RM_lib /global/scratch/users/heidihyang/001_tetragnathaTE/repeat_libs/repeatlib.fa -cpu 5 -genome_size 1100000000 -genome_coverage 0.25 -sample_number 2 -RM_t 0.2

Any ideas as to how I can resolve this issue? Thanks in advance!

Best,
Heidi

clemgoub commented

Hello Heidi,

I think you should try to run it in two steps. Let's say your local directory containing your reads is /global/scratch/users/heidihyang/001_tetragnathaTE

  1. Create a command file command.sh in /global/scratch/users/heidihyang/001_tetragnathaTE file that will include:
#! /bin/bash
cd /opt/dnaPipeTE
python3 dnaPipeTE.py -input /mnt/01_data_from_jose/001_F.fastq.gz -output /mnt/test_001_output/ -RM_lib /mnt/001_tetragnathaTE/repeat_libs/repeatlib.fa -cpu 5 -genome_size 1100000000 -genome_coverage 0.25 -sample_number 2 -RM_t 0.2

/mnt is the directory in the container where your local directory will be mounted. It will be equivalent to /global/scratch/users/heidihyang/001_tetragnathaTE

  1. Use a generic command to launch the singularity container, binds the input/output folder and execute the aforementioned command file.
singularity exec --bind /global/scratch/users/heidihyang/001_tetragnathaTE:/mnt /global/scratch/users/heidihyang/sing_DPTE/dnapipete.img /mnt/command.sh

Let me know how it goes!

Cheers,

Clément

heidihyang commented
clemgoub commented

Hello Heidi!

To confirm, you have the "permission denied" issue when you try to run

singularity exec --bind /global/scratch/users/heidihyang/001_tetragnathaTE:/mnt /global/scratch/users/heidihyang/sing_DPTE/dnapipete.img /mnt/command.sh

If, yes, it may be that command.sh is not executable, you can try to chmod+x command.sh before launching the singularity exec command.

The main issue with the initial command, is that dnaPipeTE cannot be executed outside of its folder (/opt/dnaPipeTE) and you need to change directory before executing the dnaPipeTE command. That's why it is more convenient to use the command.sh file.

Let me know how it goes! If you still have permission issue, I will try to figure out how to run it all in one command!

Cheers,

Clém

clemgoub commented

Please reopen if further assistance is needed! Best, Clément