nucmer error in running test data

[BaiweiLo]

Hi, I installed OPERA-MS without error. But the test data result had some problems. First, there were differences in the assembled contig length.

3,8c3,8
< *** *** Assembly size: 1642270 bp
< *** *** Max contig size: 188904 bp
< *** *** Contig(s) longer than 1Mbp: 0
< *** *** Contig(s) longer than 500kbp: 0
< *** *** Contig(s) longer than 100kbp: 2
< *** *** Contig N50: 71524 bp

*** *** Assembly size: 9469736 bp
*** *** Max contig size: 2708688 bp
*** *** Contig(s) longer than 1Mbp: 2
*** *** Contig(s) longer than 500kbp: 3
*** *** Contig(s) longer than 100kbp: 13
*** *** Contig N50: 759045 bp

Second, I noticed several error message inside the log.err file

cat: '/home/hurngyi/Downloads/OPERA-MS/sample_output//intermediate_files/strain_analysis/*/excluded_contigs.fa': No such file or directory
rm: cannot remove '/home/hurngyi/Downloads/OPERA-MS/sample_output//intermediate_files/strain_analysis': No such file or directory
rm: cannot remove '/home/hurngyi/Downloads/OPERA-MS/sample_output//scaffoldSeq.fasta': No such file or directory
rm: cannot remove '/home/hurngyi/Downloads/OPERA-MS/sample_output//scaffoldSeq.fasta.stats': No such file or directory

And lastly, the was a nucmer.error file with these messages inside
20190430|183117| 11845| ERROR: The following critical files could not be used
20190430|183117| 11845| /home/hurngyi/Downloads/OPERA-MS/sample_output/intermediate_files/opera_long_read/GAPFILLING/opera_scaffold_11/racon_remapped.fasta
20190430|183117| 11845| Check your paths and file permissions and try again

I checked the dependencies and they all seemed fine. I also tried to execute the program with root to avoid permission issues, but ended up with the same error.

Thank you for your help

[dbertran78]

Hi JohnsonStev,
I will need your complete log files to identify the problem:

1. the complete log.err
2. the detail logs OPERA-MS-LOG.tar.gz that can be obtained using the following command lines:
   cd /home/hurngyi/Downloads/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/;

You can send me the files at [email protected]

Best regards,

--- Denis

[BaiweiLo]

Hi Denis,
Did you receive my mail?

Best~

[dangchenyuan]

I also meet the same error in the running of test data, but when I run it the second time, the nucmer error was disappeared. what's wrong? @dbertran78

[TongChengxuan]

I also meet the same error in the running of test data, but when I run it the second time, the nucmer error was disappear. what's wrong?

Hi Chenyuan,
Can you please send your command line used and log files.
To obtain log files, run: OPERA-MS/bin/get_log.sh OPERA-MS/test_files/RESULTS/
OPERA-MS-LOG.tar.gz will be create in your working directory.

Please send OPERA-MS-LOG.tar.gz, command lines used to and the nucmer error you encountered to [email protected] and [email protected]

[dangchenyuan]

I also meet the same error in the running of test data, but when I run it the second time, the nucmer error was disappear. what's wrong?

Hi Chenyuan,
Can you please send your command line used and log files.
To obtain log files, run: OPERA-MS/bin/get_log.sh OPERA-MS/test_files/RESULTS/
OPERA-MS-LOG.tar.gz will be create in your working directory.

Please send OPERA-MS-LOG.tar.gz, command lines used to and the nucmer error you encountered to [email protected] and [email protected]

THX. I will try it.

[iek]

Any luck with this issue? I am also having a similar issue.