I run this useful tool and an error occurs

chsmiss / ATAC-amp

Searching for co-amplified regions on the genome from ATAC-seq data

MIT License

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I run this useful tool and an error occurs #2

Open chaiepi opened 7 months ago

chaiepi commented 7 months ago

Hi, I run this useful tool and an error occurs as follows: Traceback (most recent call last): File "/ATAC-amp/AtacAmp.py", line 303, in split_bk_dir = process_split_reads(split_bam_f) File "/ATAC-amp/AtacAmp.py", line 137, in process_split_reads breakpoint_start = split_line.pos + int(split_line.cigarstring.split('M')[0]) ValueError: invalid literal for int() with base 10: '1I102'

So how to fix it?

Thanks in advance

chsmiss commented 7 months ago

Thank you for your feedback, this problem is caused by the inaccurate recognition of reads with INDEL in the previous version of ATACAmp, we have made some modifications, please download the programme again and run it, if you have any problems, please feel free to contact us!

chaiepi commented 7 months ago

Thank you for your feedback, this problem is caused by the inaccurate recognition of reads with INDEL in the previous version of ATACAmp, we have made some modifications, please download the programme again and run it, if you have any problems, please feel free to contact us!

Thanks for your reply. I update ATACAmp, but one more error occurs as follow: File "/software/ATAC-amp/AtacAmp.py", line 153 'I').split('D') IndentationError: unexpected indent

chsmiss commented 7 months ago

Sorry for leaving this error, please try again now!

chaiepi commented 7 months ago

Thanks for your reply. I update ATACAmp again, but another error occurs as follow: Traceback (most recent call last): File "/software/ATAC-amp/AtacAmp.py", line 336, in split_bk_dir = process_split_reads(split_bam_f) File "/software/ATAC-amp/AtacAmp.py", line 178, in process_split_reads if operation == 'I': UnboundLocalError: local variable 'operation' referenced before assignment

chsmiss commented 7 months ago

Please try again, I believe the problem is now solved

chaiepi commented 7 months ago

No error occurs. it works! but the output file (in my case is the file of s02.pri.atac.cancer.result) has no contents. figure as follows

chsmiss commented 7 months ago

That might mean your sample doesn't have ecdna or hsr regions.Maybe you could try a sample that's positive for ecdna.

---Original--- From: @.> Date: Mon, Dec 11, 2023 10:23 AM To: @.>; Cc: @.**@.>; Subject: Re: [chsmiss/ATAC-amp] I run this useful tool and an error occurs(Issue #2)

No error occurs. it works! but the output file (in my case is the file of s02.pri.atac.cancer.result) has no contents. figure as follows

image.png (view on web)

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chaiepi commented 6 months ago

Hello, this tool outputs this error: [E::idx_find_and_load] Could not retrieve index file for 's02.pri.atac.cancer.split.bam' . Can this error influence the final results? By the way, can you provide me a test bam file that's positive for ecdna.