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avierstr / amplicon_sorter

Sorts amplicons from Nanopore sequencing data based on similarity
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Problem in tmp file not found #20

Closed cocoaawil closed 1 month ago

cocoaawil commented 5 months ago

Dear Sirs, I have some problem about tmp file which was not created. I ran the job in linux server. There is some error in below:

passedQC_iF02_iR09.fasta contains 17 reads. --> Low number of reads, reading all 17 out of 17 sequences between 1350 and 1650bp processing: file_0.todo Estimating the ssg value for this dataset Traceback (most recent call last): File "amplicon_sorter.py", line 2081, in sort_groups() File "amplicon_sorter.py", line 2000, in sort_groups grouplist = update_list(tempfile) File "amplicon_sorter.py", line 944, in update_list estimated_ssg = SSG(tempfile) # estimate ssg value File "amplicon_sorter.py", line 795, in SSG with open(tempfile, 'r') as tf: FileNotFoundError: [Errno 2] No such file or directory: 'passedQC_iF02_iR09_compare.tmp'

I'm not sure that how should I solve this problem. Could you please suggest me?

avierstr commented 5 months ago

I think the problem is the low number of reads. These are probably to different from each other for the program to find 2 or more sequences to create consensus. If you blast those reads, are they the same species ? Or are your working on an external disk or network drive like Onedrive, google drive or something like that ? That can also cause the error because there is a delay in writing and reading files.

cocoaawil commented 5 months ago

Thank you very much for your response. I tried to run one job in the same sample between two servers based on linux system. One server based on python3.6, job was completed but other server based on python3, job did not complete because of tmp not found like that. I'm not sure that It maybe python version or not.

tylerch9999 commented 1 month ago

I am having a similar issue. Macbook, using python3.12.7, and using ~1,000 reads (100bp each) from short amplicon sequencing.

avierstr commented 1 month ago

Hi Tylerch9999, Does your macbook has a M1 processor ? That can cause that error. see: https://github.com/avierstr/amplicon_sorter/issues/14 In the last comment there, I have put a extra version you can donwload with an extra command option (-mac). Can you try if that solves the problem ? Best regards, Andy

avierstr commented 1 month ago

I have now added an single core version that should work: amplicon_sorter_single.py