Python error

[P4sm]

Hi,

I got an error while running VarSimLab with the default settings. Here's the SIMULATION_IS_COMPLETE.txt log file:

SIMULATION_IS_COMPLETE.txt

[abdelrahmanhosny]

Make sure that the docker container is running from a folder that it has a write permission to. If you are using Windows, this should be some directory under C drive.

[P4sm]

Actually, I had to already edit the manifest.json file:
To
{ "reference": "hg19.fa", "targets": "hg19-targets.bed" }
from

{ "reference": “hg19.fa", "targets": “hg19-targets.bed" }
I changed the quotation marks. Otherwise the program gave me an error about the manifest file.

[P4sm]

I am using Ubuntu 16.04 LTS and I am running it as the superuser (root).

[abdelrahmanhosny]

Can you use the latest Docker image nabavilab/varsimlab:latest when you use Docker run. Make sure you have the latest image locally by using the command docker pull nabavilab/varsimlab

[P4sm]

And according to the log file the program completed some of the first steps, and it managed to write to the folder I am using.

[P4sm]

I just used this run.sh script:

docker stop varsimlab
docker rm varsimlab
docker run -v $(pwd):/ref -p 8000:8000 --name varsimlab nabavilab/varsimlab

and it loads VarSimLab v0.0.2

[abdelrahmanhosny]

What are the output files you get? What are their sizes?

[P4sm]

normal/
SIMULATION_IS_COMPLETE.txt
tumor/

normal/

normal_all_reads.fastq 4,9M

tumor/

tumor_all_subclones_reads.fastq 0
subclone_1/

tumor/subclone_1/

INDELs_1.txt 7,5M
INDELs_2.txt 7,5M
SNPs_1.txt 145M
SNPs_2.txt 145M

[abdelrahmanhosny]

Can you run the simulation again and let us know if you get the exact same error? The above file sizes (in megabytes) seem to be unexpected.

[P4sm]

I think the normal file is OK.

cat normal_all_reads.fastq | wc -l
80000

because I have just 10000 read pairs (20 000 reads)

[P4sm]

Yes, I got the same error and the same files again

[P4sm]

Before the error I had these files in tumor/subclone_1/

-rwxr-xr-x 1 root root 3157608038 loka 12 18:03 hg19.fa
-rw-r--r-- 1 root root 7868416 loka 12 18:20 hg19.fa_INDELs_S_0.0020_I_0.0001_C_2.00_1000_150000_1.txt
-rw-r--r-- 1 root root 7856128 loka 12 18:20 hg19.fa_INDELs_S_0.0020_I_0.0001_C_2.00_1000_150000_2.txt
-rw-r--r-- 1 root root 151148029 loka 12 18:18 hg19.fa_SNPs_S_0.0020_I_0.0001_C_2.00_1000_150000_1.txt
-rw-r--r-- 1 root root 151148029 loka 12 18:18 hg19.fa_SNPs_S_0.0020_I_0.0001_C_2.00_1000_150000_2.txt
-rw-r--r-- 1 root root 3157860352 loka 12 18:21 Indel_1.fa
-rw-r--r-- 1 root root 3157864448 loka 12 18:21 Indel_2.fa
-rw-r--r-- 1 root root 7852032 loka 12 16:45 INDELs_1.txt
-rw-r--r-- 1 root root 7860224 loka 12 16:45 INDELs_2.txt
-rw-r--r-- 1 root root 3157608088 loka 12 18:18 SNP_OUT_1.fa
-rw-r--r-- 1 root root 3157608088 loka 12 18:18 SNP_OUT_2.fa
-rw-r--r-- 1 root root 151148029 loka 12 16:43 SNPs_1.txt
-rw-r--r-- 1 root root 151148029 loka 12 16:43 SNPs_2.txt

And according to the log file the program is looking for /ref/my_sim/tumor/subclone_1/allele_1.fa
which doesn't exist

[P4sm]

I tried just the chromosome 1 of hg19 and no error this time.
SIMULATION_IS_COMPLETE.txt

And I actually reinstalled docker, so now I can try with the whole hg19 reference.

[P4sm]

Yes, I got the same error again with the whole reference. Perhaps my computer ran out of memory? How much RAM should be enough for this?

[Eric4Wu]

I have same issue that chr1 did but whole chromosome did not simulate the reads, what does this message stands for : "Wait! Wait! Simulating the variations in subclone 1 is complete. But it's still generating reads ..
Cleaning temporary files .." , it appears before allele_1.fa simulation step, and the next run the system can't find allele_1.fa then terminate the whole simulation. why whole chromosome simulation put this message before the allele.fa simulation ?

[abdelrahmanhosny]

@Eric4Wu Perhaps whole genome simulation suck up all the memory you have and get stuck at some point. I think it would be better to simulate on a single chromosome, not the whole genome.