"Index out of range" Error in read_analysis.py about nanosim

[cheny19]

I randomly downloaded one flowcell from the Nanopore WGS Consortium NA12878 and tried V2.1.0, but cannot re-produce the error. Could you send me your dataset so I can debug? Thanks!

[zhouanbo]

Thanks for the reply! Sure, the command I'm using is

python3 /lab01/Tools/NanoSim/src/read_analysis.py -I /nfs/.../rel3-nanopore-wgs-152889212-FAB45271.fasta -r /nfs/.../GRCh38_full_analysis_set_plus_decoy_hla.fa

I also randomly picked a file, the link is

http://s3.amazonaws.com/nanopore-human-wgs/rel3-nanopore-wgs-152889212-FAB45271.fastq.gz

I then gunzipped it and used seqtk to convert to fasta:

./seqtk seq -a /nfs/.../rel3-nanopore-wgs-152889212-FAB45271.fastq > /nfs/.../rel3-nanopore-wgs-152889212-FAB45271.fasta

[cheny19]

I downloaded the above file and converted it, but still, I didn't see any error. Our commands differ in the following steps:

1. ./seqtk seq I used -A instead of -a because the version I used doesn't have -a option. Please check your fasta file and make sure it's correct.

2. The reference genome maybe different. Mine doesn't have any patches, only 24 chromosomes. I don't think it should cause the problem, but try to remove the patches and give it a shot.

3. read_analysis.py actually don't have -I option, it's actually -i, although I don't think it's the reason either.

Also, please check if your minimap2 run succeeded and make sure the .sam file is not empty. If you still can't get rid of the error, please share your alignment file and I'll start from there.

[zhouanbo]

Hi Chen,
Sorry the LAST alignment took a few days.
I did two things:

1. I first used NanoSim 1.3.0 which has the read_analysis.py unmodified, and it processed the same fasta file ok.
2. I cut the first 100 line from fasta the file, and ran with NanoSim 2.1.0, it also runs ok.

So I think there should be something in the fasta file that's incompatible. To check the file is alright, I downloaded it again and went through the same procedure, the md5sum checks out, it's 1c1bb3fd8625cbb45e41c058422923ed. I'm also attaching a link of that file from google drive for your reference: https://drive.google.com/open?id=1dSEeMGrF64zFVnJfvI6ENnc-By8K_PeH

Thanks again for your help!
Anbo.

[cheny19]

I downloaded your attached fasta file and again, it worked for me. I suspect it's either Python or package incompatibility issue. My Python version is 3.6.3 and I also uploaded a requirements.txt to this repo, including some key packages used in NanoSim 2.1.0. Please download the txt file and install them using conda with the command conda install --yes --file requirements.txt. Let me know how it works. And I'd also like to know the versions of your packages so I can improve NanoSim. Thanks!

[zhouanbo]

Hi,
I have the package version as following:
python (3.6.3)
HTSeq (0.10.0)
numpy (1.14.5)
pybedtools (0.7.10)
pysam (0.14.1)
scipy (1.1.0)
six (1.11.0)
I ran NanoSim on another server and it runs successfully. I suspect it's because I'm running it on Centos 6.3 and the system is too old.
Thanks for the help tho!