Primary informations
Username:evan9
Cluster: baobab
Description
I recently obtained my access and for some reasons things do not go for me as for my PI on his own session. When i try to run samtools or bowtie for my analysis, i get an error message telling me that some library file do not exist
Steps to Reproduce
/srv/beegfs/scratch/shares/brauns_lab/data/sequencing_data/nathan/BAM
type: sbatch makebam.sh
Expected Result
in BAM: a file called ***.raw.bam
Actual Result
I get an error message:
sbatch: error: Batch script is empty!
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = “fr_FR.UTF-8”
are supported and installed on your system.
perl: warning: Falling back to the standard locale (“C”).
/srv/beegfs/scratch/shares/brauns_lab/Tools/samtools-1.12/samtools: error while loading shared libraries: libbz2.so.1.0: cannot open shared object file: No such file or directory
(ERR): bowtie2-align died with signal 9 (KILL)
slurmstepd: error: Detected 1 oom_kill event in StepId=6021107.batch. Some of the step tasks have been OOM Killed.
I tried, as suggested by my PI, to use load module GCC/8.3.0 and SAMtools/1.10 and also for bowtie to see if it changes something.
I still get the same result
Thank you in advance
Dear Nathan,
It seems the bowtie2 software is not compiled correctly. But we propose a lot of precompiled bowtie software on the cluster
(baobab)-[root@login2 ~]$ ml spider bowtie
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Bowtie:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
Versions:
Bowtie/1.1.2
Bowtie/1.2.2
Bowtie/1.3.0
Bowtie/1.3.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "Bowtie" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Bowtie/1.3.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Bowtie2:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at
aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
gapped, local, and paired-end alignment modes.
Versions:
Bowtie2/2.3.2
Bowtie2/2.3.4.1
Bowtie2/2.3.4.2
Bowtie2/2.3.5.1
Bowtie2/2.4.4
Bowtie2/2.4.5
Bowtie2/2.5.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "Bowtie2" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider Bowtie2/2.5.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Could you please try again by using one of those, idealy the last one?
Best regards,
I loaded bowtie2/2.5.1
now the erorr message is different:
sbatch: error: Batch script is empty!
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = (unset),
LANG = “fr_FR.UTF-8”
are supported and installed on your system.
perl: warning: Falling back to the standard locale (“C”).
(ERR): bowtie2-align died with signal 9 (KILL)
[main_samview] fail to read the header from “-”.
slurmstepd: error: Detected 1 oom_kill event in StepId=6021708.batch. Some of the step tasks have been OOM Killed.
I can also add that when i run the command using only bash and not sbatch (with the sbatch in the script also commented) this seems to work but take too much time
Hi,
why are you using your own version of bowtie and samtools instead of the one we provide?
This is my recommendation:
(baobab)-[sagon@login2 ~]$ ml GCCcore/11.3.0 SAMtools/1.16.1 Bowtie2/2.4.5
Please share you sbatch.
But this is wrong: doing so, you are running your job on the login node instead of using a compute node and it is forbidden.
Oh sorry i didn’t know it was forbidden.
here is the code with the sbatch:
#!/bin/sh
sbatch --open-mode=append --time=12:00:00 --mem=40G --partition=shared-cpu -n 1\
-N 1 -c 8
/srv/beegfs/scratch/shares/brauns_lab/Tools/bowtie2-2.4.4/bowtie2 -p 8 --maxins 2000 -N 1 -x /srv/beegfs/scratch/shares/brauns_lab/data/\
indexes/Bowtie2/mm10/mm10 -1 /srv/beegfs/scratch/shares/brauns_lab/data/sequenc\
ing_data/nathan/CUTADAPT/6ESInh*_R1_001.fastq.gz -2 /srv/beegfs/scratch/shares/\
brauns_lab/data/sequencing_data/nathan/CUTADAPT/6ESInh*_R2_001.fastq.gz | /srv/\
beegfs/scratch/shares/brauns_lab/Tools/samtools-1.12/samtools view -b -h -o /sr\
v/beegfs/scratch/shares/brauns_lab/data/sequencing_data/nathan/BAM/6ESInh.raw.b\
am
I use the bowtie and samtools that way because it is how the pipeline of the lab is written (it is not my code)
admin edit: code formating
Dear Nathan,
If you wish to use module Bowtie2 you have to correct the path of executable in your script :
(baobab)-[rossigng@login2 ~]$ ml GCC/12.2.0 Bowtie2/2.5.1
(baobab)-[rossigng@login2 ~]$ which bowtie2
/opt/ebsofts/Bowtie2/2.5.1-GCC-12.2.0/bin/bowtie2
So replace :
/srv/beegfs/scratch/shares/brauns_lab/Tools/bowtie2-2.4.4/bowtie2
By :
/opt/ebsofts/Bowtie2/2.5.1-GCC-12.2.0/bin/bowtie2
Or just :
bowtie2
Samtools is available in the cluster with the same process
(baobab)-[rossigng@login2 ~]$ ml spider samtools
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
SAMtools:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Description:
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Versions:
SAMtools/1.3
SAMtools/1.5
SAMtools/1.9
SAMtools/1.10
SAMtools/1.12
SAMtools/1.13
SAMtools/1.16.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "SAMtools" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider SAMtools/1.16.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ml GCCcore/11.3.0 SAMtools/1.16.1
Best regards,
1 Like
Dear @Nathan.Evan
Well… extra work for you:) At least you are aware that we provide those software and we keep them updated.
About your sbatch script:
Your are calling sbatch
from inside your sbatch ? This is why you have the error about “empty sbatch” and none of the arguments are used.
The way to proceed is:
- write an sbatch script
my_sbatch.sh
#/bin/sh
#SBATCH --time=12:00:00
#SBATCH --mem=40G
#SBATCH --partition=shared-cpu
#SBATCH --cores-per-task=8
srun /srv/beegfs/scratch/shares/brauns_lab/Tools/bowtie2-2.4.4/bowtie2 <your arguments>
- launch your sbatch:
sbatch my_sbatch.sh