test-run stops after reference based clustering (5/8) #39
Comments
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Hi Taylor, Please execute bin/get_log.sh. This will generate a file, please send it to us, so that we can figure out what is causing the error. Regards, |
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Dear Chengxuan,
Thank you for your quick reply.
I ran this file and it resulted in this output:
readlink: missing operand
Try 'readlink --help' for more information.
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
cp: failed to get attributes of '/intermediate_files': No such file or directory
rm: cannot remove 'OPERA-MS-LOG.tar.gz': No such file or directory
OPERA-MS-LOG/
However in my test_files/RESULTS/ folder there is an intermediate_files/ directory.
All the best
Taylor
…--
Taylor Priest
PhD Student
Molecular Ecology
Max-Planck-Institut für Marine Mikrobiologie
Celsiusstr. 1 - D-28359 Bremen - Raum 2225
Telefon: +49 421 2028-936
E-Mail: [email protected]
-----Original message-----
From: Tong Chengxuan <[email protected]>
Sent: Friday 10th April 2020 15:44
To: CSB5/OPERA-MS <[email protected]>
Cc: Taylor Priest <[email protected]>; Author <[email protected]>
Subject: Re: [CSB5/OPERA-MS] test-run stops after reference based clustering (5/8) (#39)
Hi Taylor,
Please execute bin/get_log.sh. This will generate a file, please send it to us, so that we can figure out what is causing the error.
Regards,
Chengxuan
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Hi Taylor, It seems that you did not give correct output path, please send us the command you had executed. Best regards, |
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Hi Chengxuan,
As I was performing the test run, I simply copied the suggested script from the github page:
perl ../OPERA-MS.pl --contig-file contigs.fasta --short-read1 R1.fastq.gz --short-read2 R2.fastq.gz --long-read long_read.fastq --out-dir RESULTS 2> log.err
Could the error be indicating a problem with my installation/set-up? As I said, I tried to set all dependencies up in a conda environment and then install opera-ms. I chose this option because when running the 'make' command it kept crashing when trying to install mummer. When running the check_dependencies command everything appears okay, but this doesn't check for all of the core scripts and files within the OPERA-MS directory.
Best regards,
Taylor
…--
Taylor Priest
PhD Student
Molecular Ecology
Max-Planck-Institut für Marine Mikrobiologie
Celsiusstr. 1 - D-28359 Bremen - Raum 2225
Telefon: +49 421 2028-936
E-Mail: [email protected]
-----Original message-----
From: Tong Chengxuan <[email protected]>
Sent: Monday 13th April 2020 7:49
To: CSB5/OPERA-MS <[email protected]>
Cc: Taylor Priest <[email protected]>; Author <[email protected]>
Subject: Re: [CSB5/OPERA-MS] test-run stops after reference based clustering (5/8) (#39)
Hi Taylor,
It seems that you did not give correct output path, please send us the command you had executed.
Best regards,
Chengxuan
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.
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Hi Taylor, To generate the log files, you have to give the path to your OPERA-MS output directory, a sample command line will be: Best regards, |
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Hi Chengxuan, Apologies for that. I ran the command you sent and checked the log file, which then said to check another log file in the reference clustering step, which then said to check the MUMMER log file. After looking into this log file it then shows this: /taylor/software/operams/OPERA-MS//utils//MUMmer3.23/nucmer: not found So it seems that nucmer is missing. This was installed with MUMMER in to my conda environment, but it appears that despite it being in my environment, operams is only looking in the /utils/ folder. Many thanks |
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Hi Taylor, Yes OPERA-MS will install MUMmer in the utils directory, it seems that the installation was failed. Did you observe any error during the "make" stage? Best regards, |
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Hi Chengxuan, Yes, during the make stage, it failed when installing mummer due to the program trying to link to a package that is available elsewhere in my system. For this reason, I installed all of the external programs into a conda environment and ensured that opera recognised by using the CHECK_DEPENDANCIES command. However, it seems that although opera recognises these programs, it will still only look inside the utils folder when it comes to executing a command. Perhaps I should copy the scripts from the external programs that are currently in a conda folder and place them in the utils folder and try rerunning. All the best |
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Hi Chengxuan, So i have made some changes on my system to remove the other file that mummer was trying to link to. I then re-installed operms and reran 'make'. This time there were no errors and everything was successfull. I ran CHECK_DEPENDENCY and everything is functional: *** OPERA-LG functional *** All compiled software are functional. I tried to run the test dataset again, and now it failed on step 3/8. The log files directed me to the preprocessing of reads log and there it says: [main] Real time: 5.973 sec; CPU: 5.588 sec Sorry for having so many problems. Many thanks for your help |
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Hi Taylor, Please send OPERA-MS-LOG.tar.gz to [email protected] and [email protected] Chengxuan |
Hello,
Yesterday I installed the opera-ms package but tried to do so using a conda environment. To do this, I created a conda environment, downloaded all of the necessary programs that opera-ms requires and used cpanm to install the necessary perl modules before unpacking the opera-ms directory.
When running the 'CHECK_DEPENDENCY' command, everything came back 'ok' and so it appears that there is no problems.
I then ran the test-files as recommend on the github page. The first 4 seem to run fine and then on step 5/8 - the reference based clustering, the program stopped running without any error codes being produced.
When checking the contents of the RESULTS/ file, there is an intermediate_files/ directory and a opera-ms.config file, indicating that it crashed during step 5 and didn't complete all steps. Without an error code or log file I can not seem to figure out what the problem is.
Do you have any suggestions on what may have caused this?
Many thanks in advance
Taylor
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