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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Use of uninitialized value in require at (eval ..) line 1. #204

Closed thorellk closed 8 years ago

thorellk commented 9 years ago

Hi!

I get this recurring error message, also in the newest version.

I ran with -v option to get a bit more info on when it is happening and it seems to be in the end of the FastTree part.

2015/11/13 09:40:24 Running command: /usr/local/bin/FastTree -fastest -nt accessory_binary_genes.fa > accessory_binary_genes.fa.newick FastTree Version 2.1.8 SSE3, OpenMP (4 threads) Alignment: accessory_binary_genes.fa Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000 Search: Fastest+2nd +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.50 ML Model: Jukes-Cantor, CAT approximation with 20 rate categories Initial topology in 0.00 seconds Refining topology: 0 rounds ME-NNIs, 2 rounds ME-SPRs, 0 rounds ML-NNIs Total branch-length 0.000 after 0.00 sec Total time: 0.00 seconds Unique: 1/16 Bad splits: 0/0 Aligning each cluster Use of uninitialized value in require at (eval 1957) line 1.

The next thing that happens is: 2015/11/13 09:41:08 Running command: protein_alignment_from_nucleotides -v pan_genome_sequences/acdA.fa pan_genome_sequences/ackA.fa pan_genome_sequences/acpP.fa pan_genome_sequences/acyP.fa pan_genome_sequences/addA.fa pan_genome_sequences/adh.fa pan_genome_sequences/adk.fa pan_genome_sequences/ahpC.fa pan_genome_sequences/alaS.fa pan_genome_sequences/alr.fa

After this it continues to run and finishes without further complaints and I wonder if the error is something that one should be concerned about?

Best wishes, Kaisa

andrewjpage commented 8 years ago

Fixed in 3.5.3

xiaohai90 commented 8 years ago

Dear Andrew,

When I used the roary-3.6.1, command: roary -e --mafft -p 8 *.gff I got the error: "Use of uninitialized value in require at (eval 1157) line 1.".
I checked the output files and compared with those listed on "https://sanger-pathogens.github.io/Roary/", and they were all generated but one "accessory_binary_genes.fa.newik". There is a empty file named "accessory_binary_genes.fa" in my result.

Could you please help me with this issue?

Best Regards! xiaohai

rbutleriii commented 8 years ago

Hello, I also got a similar error, but roary seems to have finished ok.

roary -p 30 -f 85/ -e -n -i 85 *.gff ##returns "Use of uninitialized value in require at (eval 61054) line 1."

Only happens if I add mafft option. Roary version 3.6.2.

andrewjpage commented 8 years ago

It is a warning rather than an error so probably safe to ignore. Usually upgrading your perl modules makes it go away. Andrew

On 17 July 2016 at 20:41, Robert Butler notifications@github.com wrote:

Hello, I also got a similar error, but roary seems to have finished ok.

roary -p 30 -f 85/ -e -n -i 85 *.gff ##returns "Use of uninitialized value in require at (eval 61054) line 1."

Only happens if I add mafft option. Roary version 3.6.2.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/sanger-pathogens/Roary/issues/204#issuecomment-233199869, or mute the thread https://github.com/notifications/unsubscribe-auth/AABeV9Qdf8Va6vMngrUDtALnERfK-WqVks5qWoVwgaJpZM4GizWI .

rbutleriii commented 8 years ago

Thanks for the help.