Use of uninitialized value in addition (+) (error?)

[jarrodscott]

Hi there

I am actually not sure if this is an error or just a warning. I reinstalled Virsorter using the conda virtual environment instructions. Everything looks fine and seems to run fin but after step 5 I get this line:

Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 873.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 875.
Use of uninitialized value in addition (+) at /home/scottjj/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 719, <$_[...]> line 877.

This repeats roughly 8000 more times where only the second instance of "line" changes

I tried to track down the meaning of this error but I could not come up with anything specific. Thoughts?

Here is my command... wrapper_phage_contigs_sorter_iPlant.pl -f contigs.fa --ncpu 25 --db 2 --wdir VIRSORTER --data-dir virsorter-data/ --diamond

[jarrodscott]

Hi! It's me again :) I wanted to add that I get the same message on two smaller datasets. I am attaching the standard outputs for each run.

\virsorter_log1.txt virsorter_log2.txt

.

[simroux]

Hi Jarrod,

The good news is that it's only a warning and should not have any impact on the result itself. Not so good news is that I was sure this had been fixed :-/ Do you remember when VirSorter was installed, and if this wasn't in the last 2 month, could you update from the latest version on this repo and try again ?

Thanks ! Best, Simon

[jarrodscott]

Hi Simon,

Nice. I like the balance between good and bad news :) Moderately amusing, it looks like I reinstalled Virsorter on Oct 13 and your last commit was Oct 19. I was looking at the general repo time stamps, which is "2 months ago". I just assumed I had the latest version. Sorry for the distraction!

I will install, run again, and report what I find.

Best, Jarrod

On Fri, Dec 6, 2019 at 11:24 AM simroux notifications@github.com wrote:

Hi Jarrod,

The good news is that it's only a warning and should not have any impact on the result itself. Not so good news is that I was sure this had been fixed :-/ Do you remember when VirSorter was installed, and if this wasn't in the last 2 month, could you update from the latest version on this repo and try again ?

Thanks ! Best, Simon

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/simroux/VirSorter/issues/58?email_source=notifications&email_token=AD3RFNSXLENT6CVCORUVDETQXJ4FBA5CNFSM4JVZBGQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGETO2Y#issuecomment-562640747, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD3RFNTWS2WIYHSODTDG4GDQXJ4FBANCNFSM4JVZBGQA .

[jarrodscott]

Ok, I am still getting this message. Here is what I did ...

conda create --name virsorter -c bioconda mcl=14.137 muscle blast perl-bioperl perl-file-which hmmer=3.1b2 perl-parallel-forkmanager perl-list-moreutils diamond=0.9.14
conda activate virsorter
git clone https://github.com/simroux/VirSorter.git
cd VirSorter/Scripts/
make clean
make
conda install --name virsorter -c bioconda metagene_annotator 

First attempt at running gave me the Bio::Seq error, so I ran perl -e "use Bio::Seq;" and got an error. So I followed this recipe from [issue #31] (https://github.com/simroux/VirSorter/issues/31#issuecomment-554087415) and everything ran smoothly except for the warning. I will try again without the Bio::Seq fix from #31.

job_02_run_virsorter_test.log

[simroux]

Thanks for testing, I'll look into it. I don't think this is due to Bio::Seq, so the fix should not have caused any issue. I think I know why this is happening, but need to do further tests, I'll let you know when a fix is ready !

[simroux]

Hi Jarrod,

I have a hard time reproducing the warning, could you share an example of a sequence id for your contig, and or some part of your input file ?

Thanks !

[jarrodscott]

Hi Simon,

Here is the dataset I used that corresponds to the log file I sent earlier. It was generated from an anvio db. I am here for the rest of the day :)

On Fri, Dec 6, 2019 at 1:56 PM simroux notifications@github.com wrote:

Hi Jarrod,

I have a hard time reproducing the warning, could you share an example of a sequence id for your contig, and or some part of your input file ?

Thanks !

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/simroux/VirSorter/issues/58?email_source=notifications&email_token=AD3RFNX7SAF7MBTYTRQ652LQXKN4DA5CNFSM4JVZBGQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGFAWZY#issuecomment-562695015, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD3RFNUGJZQUXJFFTF67QFLQXKN4DANCNFSM4JVZBGQA .

[simroux]

Hi Jarrod,

Sorry, it seems like enclosing files to email reply doesn't work as intended (at least I don't see a file linked to your last reply). If easier, you can send it directly to siroux1 at gmail

[simroux]

Hi Jarrod,

Thanks for the file ! I think I've found it, and as expected it has 0 impact on the results themselves (this warning came from a last step where VirSorter checks if a lot of sequences have been predicted viral, and if so suggests that maybe running in "virome decontamination" mode would help). Whenever the time, please try the latest release I just pushed, and let me know if this helps !

Thanks again for reporting and help in troubleshooting :-)

[jarrodscott]

Hi Simon,

Ok, I just did a fresh reinstall following the recipe above and it worked like a charm! Here is the log. I will now run on my larger datasets but I think this issue is solved :) Thanks for all of the help.

job_02_run_virsorter_test.log