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annajbott / viral_track

Pipeline for programme viral track
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Some questions about CGAT pipeline STAR index #1

Open zlz6621299 opened 7 months ago

zlz6621299 commented 7 months ago

First and foremost, I would like to extend my sincere gratitude to you and your team for developing and open-sourcing the CGAT pipeline. This tool has been immensely helpful in facilitating our use of the viral-track code, which is crucial for our research work.

However, I have encountered some technical issues during its use, for which I am yet to find a solution. I am running all programs within the Windows Subsystem for Linux (WSL) environment and have established a separate conda environment there to store the required versions of various packages. Unfortunately, I am facing errors when trying to run the pipeline. The initial error is depicted in the attached screenshot, and despite trying multiple approaches, I haven't been able to resolve it.

> # 2024-03-28 17:22:41,986 INFO code location: /usr/local/lib/python3.8/dist-packages/cgatcore/pipeline
# 2024-03-28 17:22:41,987 INFO code version:
# 2024-03-28 17:22:41,989 INFO working directory is: /home/single
# 2024-03-28 17:22:41,990 INFO changing directory to /home/single
# 2024-03-28 17:22:41,992 INFO pipeline has been initialized
# 2024-03-28 17:22:41,992 INFO temporary directory is /tmp/root
Traceback (most recent call last):
  File "pipeline_viral_track.py", line 541, in <module>
    sys.exit(P.main(sys.argv))
  File "/usr/local/lib/python3.8/dist-packages/cgatcore/pipeline/control.py", line 1528, in main
    run_workflow(args)
  File "/usr/local/lib/python3.8/dist-packages/cgatcore/pipeline/control.py", line 1488, in run_workflow
    raise ValueError("unknown pipeline action %s" %
ValueError: unknown pipeline action None

Subsequently, I thought to execute the part of the code that builds the STAR index separately. However, to my dismay, I encountered a "Segmentation fault (core dumped)" error. I am uncertain if this issue is related to not providing a GTF file. At this juncture, I am unable to successfully run the code.

`root@DESKTOP-JHR4GRU:/home/single# STAR --runThreadN 6 \

--runMode genomeGenerate\ --genomeDir /home/single/index\ --genomeFastaFiles Segmentation fault (core dumped)`

annajbott commented 7 months ago

Do you have enough memory on your machine to run STAR? Have you updated the pipeline.yml file to your own specific file paths?

zlz6621299 commented 7 months ago

Dear Dr. James-Bott,

Thank you very much for your response. The issue with the code error may have been due to downloading an earlier version of the STAR program, which might have had some errors. I have now downloaded an updated version of the STAR software, and this supports my continuation with the subsequent steps. However, it's worth noting that I only used the covid-19 and human reference genomes to build an index and perform alignments. In multiple datasets, the count values corresponding to the covid-19 genome are zero. Following this, I used the original data from GSE145926, as mentioned in the article, and performed demultiplexing before alignment, but still, I am unable to get the correct count values. The data I used is SRR11181956, corresponding to a patient with a severe COVID-19 infection, and theoretically, there should be some results.In addition, when I analyzed the raw data of EBV-related GSE158275, I was able to accurately extract EBV fragments, which I found very confusing. I have provided the reference genome I used, as well as the resulting output files, and look forward to your guidance on this matter.

Best regards,

Lizhong

发件人: Anna James-Bott @.> 发送时间: 2024年3月29日 0:25 收件人: annajbott/viral_track @.> 抄送: zlz6621299 @.>; Author @.> 主题: Re: [annajbott/viral_track] Some questions about CGAT pipeline STAR index (Issue #1)

Have you tried running the commands outside of the pipeline framework? Do you have enough memory to run STAR?

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