Error during tilling generation. Please see /XXX/XXX/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out and /XXX/XXX/XX/XXX/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err for details.

[Caiyulu-818]

Error during tilling generation. Please see /data2/bma/lcy/nanopore/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.out and /data2/bma/lcy/nanopore/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/tilling_1.err for details.

tilling_1.err :Error in during nucmer.

above is the message of error, but when perl check-dependency, all is functional, include the mummer.

[jsgounot]

Hi Caiyulu,

In this directory /data2/bma/lcy/nanopore/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/mummer/, you should have these files :

• cmd_delta_filter.txt
• cmd_delta.txt
• cmd_coord.txt

which contain the mummer command lines. Could you run one command line from the cmd_delta.txt file to see if an error is raised ?

Regards,
Jean-Sebastien

[Caiyulu-818]

Hi Caiyulu,

In this directory /data2/bma/lcy/nanopore/assemblyA1_/intermediate_files/opera_long_read/GAPFILLING/TILLING/mummer/, you should have these files :

• cmd_delta_filter.txt
• cmd_delta.txt
• cmd_coord.txt

which contain the mummer command lines. Could you run one command line from the cmd_delta.txt file to see if an error is raised ?

Regards,
Jean-Sebastien

the error message：Can't locate Foundation.pm in @inc (@inc contains: /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts /data1/xxx/perl5/lib/perl5 /xxx/xxx/perl5/lib/perl5/x86_64-linux-thread-multi /data2/xxx/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /data2/xxx/new_application/OPERA-MS/tools_opera_ms/MUMmer3.23/nucmer line 19.
BEGIN failed--compilation aborted at /data2/xxx/new_application/OPERA-MS/tools_opera_ms/MUMmer3.23/nucmer line 19.

[jsgounot]

Strange, the script should be in this directory : /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts. Could you list files inside ?

[Caiyulu-818]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } hellohere are the list files in the directory : /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts lucyncs123 ***@***.*** 签名由 网易邮箱大师 定制 On 05/31/2021 10:17，GOUNOT ***@***.***> wrote： Strange, the script should be in this directory : /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts. Could you list files inside ? —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

[jsgounot]

Sorry, is it empty ?

[Caiyulu-818]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } oh, no, you can see the picture in the attachment. lucyncs123 ***@***.*** 签名由 网易邮箱大师 定制 On 05/31/2021 ***@***.***> wrote： font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } hellohere are the list files in the directory : /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts lucyncs123 ***@***.*** 签名由 网易邮箱大师 定制 On 05/31/2021 10:17，GOUNOT ***@***.***> wrote： Strange, the script should be in this directory : /xxx/xxx/application/OPERA-MS/tools_opera_ms/MUMmer3.23/scripts. Could you list files inside ? —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

[jsgounot]

Sorry, I don't see any picture here.
Can you provide an url instead ?

[Caiyulu-818]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } Sorry,  picture in the attachment lucyncs123 ***@***.*** 签名由 网易邮箱大师 定制 On 05/31/2021 10:49，GOUNOT ***@***.***> wrote： Sorry, I don't see any picture here. Can you provide an url instead ? —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

[jsgounot]

I'm really sorry but I don't have access to your attachement.
Can you please use a web host service like imgur or just copy past the directory content ?
Is there Foundation.pm in the folder at least ?

[Caiyulu-818]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } Yes，Foundation.pm is in the folder  lucyncs123 ***@***.*** 签名由 网易邮箱大师 定制 On 05/31/2021 11:09，GOUNOT ***@***.***> wrote： I'm really sorry but I don't have access to your attachement. Can you please use a web host service like imgur or just copy past the directory content ? Is there Foundation.pm in the folder at least ? —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

[jsgounot]

Ok, this means that perl is not able to load the script even though it's found in your path include directories. Sadly there are not much I can do about that, you will have to resolve this error (or ask your IT responsible) on your own since this can come from multiple origins and it is not specifically linked to OPERA-MS. See this for example and maybe as a starting point.