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PSSUN / CircCode

A Python3-base pipeline for translated circular RNA(circRNA) identification
GNU General Public License v3.0
16 stars 4 forks source link

Problem of pipeline #9

Closed luhan125 closed 4 years ago

luhan125 commented 4 years ago

Hello,

I'm using CircCode, such a powerful tool, but I have problem, every files I used here are from your example. When I run: python3 make_virtual_genomes.py -y config.yaml, the err is: No. 1 length: 281 Traceback (most recent call last): File "make_virtual_genomes.py", line 218, in main() File "make_virtual_genomes.py", line 210, in main info.make_genome() File "make_virtual_genomes.py", line 95, in make_genome self.genome += (circrna.seq 2 + polyN) TypeError: unsupported operand type(s) for : 'Seq' and 'int'

Could you give me some advice? Thank you very much!

Best,

Lu Han

luhan125 commented 4 years ago

Hello,

I have solved the previous problem, sorry about this. But now, I still have one problem, I don't know how to do. When I run: python3 make_virtual_genomes.py -y config.yaml, the err is: Segmentation fault (core dumped)

Could you give me some advice? Thank you very much!

Best,

Lu Han

PSSUN commented 4 years ago

Hi,

Thank you for using CircCode, I have never met this problem before, now I'm trying to solve this problem. Could you please show more information about your 'config.yaml' file?

Peisen Sun

luhan125 commented 4 years ago

Hello,

Thank you for your reply. This is the content of my 'config.yaml' file:

CircCode-cofig-file

This configuration file includes all possible options and files for CircCode.

Please input full path as well as for running all process.

You can submit your question by submitting issue on github or sending an e-mail

Version = 1.0

E-mail = sps@snnu.edu.cn

Date = 20 July 2019

The name of genome

genome_name: virGenome

#################

required data

#################

The path of genome file

genome_fasta: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/genome_fasta

The path of gtf file of genome

genome_gtf: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/genome.gtf

The path of ribo-seq raw reads file

raw_reads:

The path of trimmomatic.jar

trimmomatic_jar: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/requiredSoft/trimmomatic-0.38.jar

The path of Candidate circRNA

circrnas: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/circrnas

The path of adapters file

riboseq_adapters: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/riboseq-adapters.fa

Coding sequence

coding_seq: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/coding_seq.fa

Non-coding sequence

non_coding_seq: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/non_coding_seq.fa

#####################

Required location

#####################

The path of folder for storing the final result

result_file_location: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/result_file_1

The path of folder for storing temporary results

tmp_file_location: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/tmp_file_1

#################

OTHER OPTIONS

#################

The type of reads, please input single or pair

reads_type: single

ribotype

ribotype: sra

Coverage counts, DEFAULT = 10.

coverage_counts: 10

The thread to run tophat2 and SEPCtr, DEFAULT = 6

thread: 6

merge all the NGS data: T or F

merge: F

best,

Lu Han

PSSUN commented 4 years ago

In this line: The path of genome file genome_fasta: /xtdisk/guocx_group/wangql/luhan/testis/CircCode/CircCode/example/genome_fasta I noted that your genome_fasta file is genome_fasta, make sure this file is in .fasta format. Besides, could you please tell me the RAM of your computer?

luhan125 commented 4 years ago

All the files I used are from your example. I am sure this file is in .fasta format, and I also try to change the name of this file to genome.fa, but the err is the same: Segmentation fault

luhan125 commented 4 years ago

I used sever to do this. And the RAM I applyed was 90gb. I show it here:

!/bin/sh

PBS -N find

PBS -e find.err

PBS -o find.log

PBS -q core40

PBS -l mem=90gb,walltime=240:00:00,nodes=1:ppn=10

HSCHED -s A+B+C

PPN limit 10

PSSUN commented 4 years ago

Hi Lu, After testing, all the files in the example file have no problems, so this error is not caused by the error in the input file. I'm trying to reproduce this error and I will contact you in 2 days.

luhan125 commented 4 years ago

OK, thank you very much!

PSSUN commented 4 years ago

you have to increase the stack that your operating system allocates for the python process.

The way to do it is operating system dependant. In Linux, you can check with the command ulimit -s your current value and you can increase it with ulimit -s <new_value>

Try doubling the previous value and continue doubling if it does not work, until you find one that does or run out of memory.

please try this command in terminal: ulimit -S -s unlimited

PSSUN commented 4 years ago

here's another answer:

My recent annoyance with Python 3.7 on Windows Subsystem for Linux is that: on two machines with the same Pandas library, one gives me segmentation fault and the other reports warning. It was not clear which one was newer, but "re-installing" pandas solves the problem.

Command that I ran on the buggy machine. conda install pandas More details: I was running identical scripts (synced through Git), and both are Windows 10 machine with WSL + Anaconda. Here go the screenshots to make the case. Also, on the machine where command-line python will complain about Segmentation fault (core dumped), Jupyter lab simply restarts the kernel every single time. Worse still, no warning was given at all.

https://stackoverflow.com/questions/10035541/what-causes-a-python-segmentation-fault