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weir12 / DeepEdit

DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using Nanopore direct RNA sequencing
MIT License
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Error fast5Index.tmp and parse error reading ".bed.tmp" #10

Closed acarmas1 closed 1 year ago

acarmas1 commented 1 year ago

Hello,

I've been trying to use DeepEdit to detect inosines in my direct RNA reads. I've submitted this script to my server:

bash /scratch/acarmas/AtoI/test_data/DeepEdit/Getting_Started/1.Reads_extract.sh \ --SiteFile /scratch/acarmas/AtoI/preprocessing/target_site_apis.bed \ --BamPath /scratch/acarmas/AtoI/preprocessing/head_rep1_assembly.sam \ --Fast5Dir /scratch/acarmas/AtoI/fast5/fastq_head_rep1/multi_to_single/Join \ --Output /scratch/acarmas/AtoI/preprocessing/head_rep1_assembly_target_site_reads.txt

However, I'm getting this error:

grep: .fast5Index.tmp: Input/output error grep: .fast5Index.tmp: Cannot send after transport endpoint shutdown grep: .fast5Index.tmp: Cannot send after transport endpoint shutdown grep: .fast5Index.tmp: Cannot send after transport endpoint shutdown [bed_read] Parse error reading ".bed.tmp" at line 2 samtools view: Could not read file ".bed.tmp" [bed_read] Parse error reading ".bed.tmp" at line 2

I was wondering if you could help me to troubleshoot it please.

Thank you. I'm looking forward to hearing from you.

Best, Camila

weir12 commented 1 year ago

Hello Camila,

The error message you encountered suggests that there are issues with the input files and their formats. Let's go through the error messages and troubleshoot the problem step by step:

Input/output error and Cannot send after transport endpoint shutdown: These errors indicate that there might be an issue with the file system or file access permissions. Make sure that you have proper read and write permissions for the input and output files and directories. Additionally, check if the file system on your server is functioning correctly.

Parse error reading ".bed.tmp" at line 2: This error suggests that there is an issue with the format of the input BED file. Double-check the format of the BED file specified by the --SiteFile parameter. Ensure that it follows the correct BED format, including the required columns (chromosome, start position, end position, etc.). Verify if the file path is correct and accessible.

Could not read file ".bed.tmp": This error indicates that the script was unable to read the BED file. Verify that the specified BED file exists in the specified location (--SiteFile) and that it is not corrupted. Also, ensure that you have proper read permissions for the BED file.

The error messages related to ".fast5Index.tmp": These errors suggest that there might be issues with the FAST5 files or the indexing process. Check the specified --Fast5Dir directory and ensure that it contains the expected FAST5 files. Additionally, make sure that the files are not corrupted. It's possible that the indexing process encountered errors or was interrupted. You may need to regenerate the index files or verify if there are any issues with the FAST5 files themselves.

By carefully reviewing and addressing each of these potential issues, you should be able to troubleshoot the problem with the DeepEdit script. Let me know if you have any further questions or need additional assistance.

LongxianChen commented 1 year ago

Because the script produces some .tmp files, so please ensure that you have write and read permission of your working directory in which you run this command.

LongxianChen commented 1 year ago

By the way, we updated the 2.feature_extract.py file. We recommend to use this newer version script.

acarmas1 commented 1 year ago

Hello, thanks for your help, I was to able to read the bed.tmp. But I'm still getting the fast5index.tmp issues. I'm reindexing my fast5 with tombo.

I do have a question regarding the 2.feature_extract.py. For tombo I'm using this parameters: --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000. Since this is the basecall group of my reads. But in your documentation and test dataset is 001. What part of the 2.feature_extract.py script should be change to use it for 000.

acarmas1 commented 1 year ago

Also I have another question. I regenerated the tombo resquiggle index and I've been running 1.read_extract script for 1 day. However, I just got this message. image And this is how I submitted the job. image

acarmas1 commented 1 year ago

Hello, I'm still getting this error: image I was wondering if someone could help me to troubleshoot it, please.

LongxianChen commented 1 year ago

Hello, I'm still getting this error: image I was wondering if someone could help me to troubleshoot it, please.

Hi, I think this error may caused by the access permission of specific path on your server. I modified the 1.Reads_extract.sh for you, but I am not sure if it can work well on your environment. You can perform a quick test using part of your data.

acarmas1 commented 1 year ago

Hello,

I've implemented the changes 1.Reads_extract.sh, and I started to get these errors: image So I moved all my files to only one directory and ran 1.Reads_extract.sh with only one part of my data. However, it is still taking a while, it's been 2 days that has been running, and it has not finished, but so far no errors, which is good. I'll let you know once it finishes.

weir12 commented 1 year ago

Closing the issue due to inactivity for a long period of time