Error running test script

[ilyavs]

Hello,
I installed the latest version of OPERA-MS and ran the test script as instructed in the documentation. It produced the following error in log.err:
'Error in during OPERA-LG. Please see /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/opera_long_read/log.out and /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/opera_long_read/log.err for details.'

/net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/opera_long_read/log.out contained:
'Step 1: Reading configuration file ...
error reading mapping file
error reading mapping file
error reading mapping file
error reading mapping file
error reading mapping file
error reading mapping file
Time Taken: 0.000883 seconds
ERROR: Cannot open /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/reference_mapping/NO_REPEAT/filtered_pairedEdges_i0 file
'
I examined the file structure and the file filtered_pairedEdges_i0 is in /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/reference_mapping/ and not in a NO_REPEAT subfolder.

How can I fix this issue asap?

Thanks,
Ilya.

[dbertran78]

Hi Ilya,
I will need additional log files to investigate your problem.
Could you please run the following commands, and share with me the OPERA-MS-LOG.tar.gz file.
opera_res=/net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/ mkdir OPERA-MS-LOG/; cp --parent $opera_res/*/*err* $opera_res/*/*out* $opera_res/strain_analysis/*/STRAIN*/log* $opera_res/strain_analysis/*/STRAIN*/opera.config OPERA-MS-LOG/; tar -cvzf OPERA-MS-LOG.tar.gz OPERA-MS-LOG/

Best regards,

--- Denis

[ilyavs]

Hi Denis,
Thank you for your response. I ran the commands and got the following stdout:
'cp: cannot create regular file \u2018OPERA-MS-LOG/bin/canberra-boot\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/canberra-gtk-play\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/gpg-error\u2019: Permission denied
cp: cannot open \u2018/dev/stderr\u2019 for reading: Permission denied
cp: omitting directory \u2018/lib64/libcanberra-0.30\u2019
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra-gtk3.so.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra-gtk3.so.0.1.9\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra-gtk.so.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra-gtk.so.0.1.9\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra.so.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcanberra.so.0.2.5\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcom_err.so\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcom_err.so.2\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libcom_err.so.2.1\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libgpg-error.so.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libgpg-error.so.0.10.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libsamba-errors.so.1\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/grub2-mklayout\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/nl-route-add\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/nl-route-delete\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/nl-route-get\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/nl-route-list\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/plymouth\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/tcptraceroute\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/timeout\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/traceroute\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/bin/traceroute6\u2019: Permission denied
cp: cannot open \u2018/dev/stdout\u2019 for reading: Permission denied
cp: omitting directory \u2018/etc/iproute2\u2019
cp: omitting directory \u2018/etc/plymouth\u2019
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libnl-route-3.so.200\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libnl-route-3.so.200.23.0\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libshout.so.3\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/lib64/libshout.so.3.2.0\u2019: Permission denied
cp: omitting directory \u2018/lib64/plymouth\u2019
cp: omitting directory \u2018/run/plymouth\u2019
cp: cannot create regular file \u2018OPERA-MS-LOG/sbin/plymouth-set-default-theme\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/sbin/route\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/sbin/routef\u2019: Permission denied
cp: cannot create regular file \u2018OPERA-MS-LOG/sbin/routel\u2019: Permission denied
cp: failed to get attributes of \u2018/strain_analysis\u2019: No such file or directory
cp: failed to get attributes of \u2018/strain_analysis\u2019: No such file or directory
OPERA-MS-LOG/
OPERA-MS-LOG/dev/
OPERA-MS-LOG/boot/
OPERA-MS-LOG/boot/initrd-plymouth.img
OPERA-MS-LOG/proc/
OPERA-MS-LOG/proc/interrupts
OPERA-MS-LOG/lib64/
OPERA-MS-LOG/sbin/
OPERA-MS-LOG/sbin/plymouthd
OPERA-MS-LOG/bin/
OPERA-MS-LOG/bin/abrt-action-check-oops-for-hw-error
OPERA-MS-LOG/etc/
OPERA-MS-LOG/run/
'
The log file is attached.

Thanks,
Ilya.
OPERA-MS-LOG.tar.gz

[dbertran78]

It seems that you cannot declare variables on the bash interpreter you are using.

Could you try the following commands and send me OPERA-MS-LOG.tar.gz.
cd /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output/intermediate_files/; mkdir OPERA-MS-LOG/; cp --parent */*err* */*out* strain_analysis/*/STRAIN*/log* strain_analysis/*/STRAIN*/opera.config OPERA-MS-LOG/; tar -cvzf OPERA-MS-LOG.tar.gz OPERA-MS-LOG/;

Best regards,

--- Denis

[ilyavs]

Hi,
Here is the new log output.
OPERA-MS-LOG.tar.gz

Thanks,
Ilya.

[dbertran78]

Hi,
It seems that some perl modules were not correctly installed.
Could you please try to run the following command and indicate me if all the perl modules were correctly installed:
/net/mraid08/export/genie/long_read_assembly/OPERA-MS/utils/install_perl_module.pl

Regards,

--- Denis

[ilyavs]

Hi,
I think you are right. One of the modules was installed when running the command. Here is the stdout:
*** Check perl module Switch
*** Check perl module Statistics::Basic
*** Check perl module Statistics::R
*** Install perl module Statistics::R
! Configure failed for Statistics-R-0.33. See /home/ilyav/.cpanm/work/1551157640.158371/build.log for details.
--> Working on Statistics::R
Fetching http://www.cpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz ... OK
Configuring Statistics-R-0.34 ... N/A
*** Check perl module File::Which
*** Check perl module File::Spec::Functions
*** Check perl module Getopt::Long
I will rerun the test script now and report back.
Thanks,
Ilya.

[ilyavs]

Hi,
The test script failed with the same error: ERROR: Cannot open /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/reference_mapping/NO_REPEAT/filtered_pairedEdges_i0 file

Again, the file filtered_pairedEdges_i0 is in /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/reference_mapping/ and not in /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/reference_mapping/NO_REPEAT/

Moreover, please note that some of the file paths contain // instead of /. I know that it is usually harmless but I encountered issues with this on my system in the past.

Thanks,
Ilya.

[dbertran78]

Hi,
I am not able to figure out what is the problem with your run using the log files only.
Could you please do a complete archive of the test run and share it with me:
tar -cvzf OPERA-MS-RUN.tar.gz /net/mraid08/export/genie/long_read_assembly/OPERA-MS/sample_output//intermediate_files/

Best regards,

--- Denis

[ilyavs]

Hi,
The requested archive is too big to attach. Here is a dropbox link, please let me know once you download it so I can delete it. https://www.dropbox.com/s/h30dfob7754tg9k/OPERA-MS-RUN.tar.gz?dl=0
Thank you,
Ilya.

[dbertran78]

The download is completed. You can delete the file.

Regards,

--- Denis

[ilyavs]

Thanks. Looking forward to your input.
Ilya.

[ilyavs]

Hi,
Any news? I am eager to try this out :)
Thanks,
Ilya.