Error code on successful finish

[beardymcjohnface]

The program throws an exit code 1 instead of 0 when it fails to find any prophage regions.

[gancao]

I am sorry for this problem. Could you please give some details about the errors when running you data? or you could attach the input sequence file ?

[beardymcjohnface]

I think I misread the error message. It looked like it was finishing normally but there was an error message for line 2731 thread_num not defined. It wasn't happening for all of the genomes I was testing. I had changed all of the num_threads = 20 to num_threads = 1 as I wanted to benchmark with one thread; I don't know if that's related to the issue.

I managed a workaround by hard-coding thread_num of 1 like so:
line 2731: if (len(threading.enumerate()) <= int(1)):

[gancao]

I am sorry for this error. But I think this error shouldn’t occur. In addition, I think you should use the latest dbscan-swa.py and you’d better to not change the thread_num =1 I attached this script file in the following. | | 甘草 | | ***@***.*** | 签名由网易邮箱大师定制 On 12/14/2021 ***@***.***> wrote： I think I misread the error message. It looked like it was finishing normally but there was an error message for line 2731 thread_num not defined. It wasn't happening for all of the genomes I was testing. I had changed all of the num_threads = 20 to num_threads = 1 as I wanted to benchmark with one thread; I don't know if that's related to the issue. I managed a workaround by hard-coding thread_num of 1 like so: line 2731: if (len(threading.enumerate()) <= int(1)): — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[gancao]

I have corrected the possibly related code on https://github.com/gancao/DBSCAN-SWA-1 | | 甘草 | | ***@***.*** | 签名由网易邮箱大师定制 On 12/14/2021 ***@***.***> wrote： I am sorry for this error. But I think this error shouldn’t occur. In addition, I think you should use the latest dbscan-swa.py and you’d better to not change the thread_num =1 I attached this script file in the following. | | 甘草 | | ***@***.*** | 签名由网易邮箱大师定制 On 12/14/2021 ***@***.***> wrote： I think I misread the error message. It looked like it was finishing normally but there was an error message for line 2731 thread_num not defined. It wasn't happening for all of the genomes I was testing. I had changed all of the num_threads = 20 to num_threads = 1 as I wanted to benchmark with one thread; I don't know if that's related to the issue. I managed a workaround by hard-coding thread_num of 1 like so: line 2731: if (len(threading.enumerate()) <= int(1)): — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[beardymcjohnface]

Thanks, I'll try this fork. Should this fork be used in the future or will the HIT-ImmunologyLab repo be updated?

So I finished rerunning my tests and only one genome is now throwing the error. I think it is related to lines 1378-1380:

	if len(contents)==1:
		print('0 prophage region was detected in the query bacterial genome!')
		sys.exit(1)

I've attached the log file for this run below. As far as I can tell it ran error-free, found no prophages and terminated with error code 1. In this instance I think it the program should generate an empty output file and end with an exit code 0.

dbscan.log

[gancao]

I will take your advice. If no prophage is detected, the program will create an empty output file

…

---- 回复的原邮件 ---- | 发件人 | ***@***.***> | | 日期 | 2021年12月14日 12:03 | | 收件人 | ***@***.***> | | 抄送至 | ***@***.******@***.***> | | 主题 | Re: [HIT-ImmunologyLab/DBSCAN-SWA] Error code on successful finish (Issue #6) | Thanks, I'll try this fork. Should this fork be used in the future or will the HIT-ImmunologyLab repo be updated? So I finished rerunning my tests and only one genome is now throwing the error. I think it is related to lines 1378-1380: iflen(contents)==1: print('0 prophage region was detected in the query bacterial genome!') sys.exit(1) I've attached the log file for this run below. As far as I can tell it ran error-free, found no prophages and terminated with error code 1. In this instance I think it the program should generate an empty output file and end with an exit code 0. dbscan.log — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.