Hi,
I have a quick question regarding directing the path to the indexed genome folder. Following is the code I used;
hisat2 -p $threads --dta --rna-strandness RF -x /scratch/datasets/genome_indexes/other_genomes/potato/hisat2 -1 ${SAMPLE}.fq.gz -2 ${SAMPLE}.fq.gz -S ${SAMPLE}.sam
after loading the module
module load HISAT2/2.2.0-foss-2018b
I was running the script on our ADA cluster and got the following error
sh: /sw/eb/software/HISAT2/2.2.0-foss-2018b/bin/hisat2_read_statistics.py: No such file or directory (ERR): "/scratch/datasets/genome_indexes/other_genomes/potato/hisat2" does not exist Exiting now ...
Can someone help me to resolve this issue? Thanks in advance.
1 answer
I personally always try to make it as simple as possible. Copy all the fastq files into one folder and give it clear names e.g.
Sample1_1.fastq.gz Sample1_2.fastq.gz Sample2_2.fastq.gz Sample2_2.fastq.gz
Then use the simplest possible script (or learn how to use workflow managers):
Idx=path/to/idxfiles
for i in *_1.fastq.gz
do
SAMPLE=${i%_1.fastq.gz}
hisat2 (options...) -x "${Idx}" -1 ${SAMPLE}_1.fastq.gz -2 ${SAMPLE}_2.fastq.gz \
| samtools view -o ${SAMPLE}.bam
done
That's it. Eliminate unnecessary elements from your script as well as echo that indicate any kind of status. Trim it to the very necessary parts and then get it runnign. Then you can add additional things once it works.
Everything is running fine and got bam files too. :) The only exception is the following (I guess it is something to with installation at ADA cluster since I don't see such script there)
/sw/eb/software/HISAT2/2.2.0-foss-2018b/bin/hisat2_read_statistics.py: No such file or directory (ERR)
PS: Appreciate if you can point me to a good workflow management tool and tutorial for similar analysis like this.
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Output of
ls /scratch/datasets/genome_indexes/other_genomes/potato/?Based on the listing above it looks like there is no
hisat2directory. So you will need to tryMy apologies. I was using
Here is the correct output for
ls /scratch/datasets/genome_indexes/other_genomes/potato/Then simply insert
hisat2in right spot above.Sorry, I think I confused you;
The output for
ls /scratch/datasets/genome_indexes/other_genomes/potato/is (answer to ATPoint's question)When I ran the job I used the following code
Directing to the hisat2 folder and got the error mentioned in the original post.
These are not genome indices, are they? The hisat index consists of several files, e.g. genome.ht2 etc...
This is how it should look e.g. for a genome called
mm10.fa:Here it would be
-x mm10as it is the suffix of the indexed file you have to provide. it then uses these ht2 files as needed.Inside the hisat2 folder (
ls /scratch/datasets/genome_indexes/other_genomes/potato/hisat2/), there are eight files (I guess that is the default number it makes)Ah I see; that means I need to use
DM_1-3_516_R44_potato_genome_assembly.v6.1.1as follows/scratch/datasets/genome_indexes/other_genomes/potato/hisat2/DM_1-3_516_R44_potato_genome_assembly.v6.1Thank you! I will do that
Even after changing the path, I am getting the following error (I killed the job after this error to save my service units)
Prob due to a problem at cluster? (I emailed them too.... but no reply yet)
Are the fastq files in the right spot? Are those variables correctly pointing to those files?
they are in the same directory where the job is running from. I also check the file extensions too. Nothing makes sense :(
This by the way is the same file. Try simplifying your script.
Oh, Shoot! You are correct. Still learning A, B, Cs..