Please cite Roary if you use any of the results it produces:
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
MSG: G"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Use ofPubmed: 26198102
Command error:
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.28/Encode.pm line 69.
Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.28/Encode.pm line 69.
Use of uninitialized value in require at (eval 1243) line 1.
2023/01/31 16:43:06 Input file to MAFFT missing: pan_genome_sequences/group_6.fa
2023/01/31 16:43:06 Input file to MAFFT missing: pan_genome_sequences/group_6.fa
cat: pan_genome_sequences/group_6.fa: No such file or directory
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
Use of uninitialized value $gene_length in addition (+) at /usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm line 36.
Work dir:
/mnt/c/users/giese/documents/ubuntu/ciano_anta/work/66/c30290a91d09b2837a65a7dd2a6fa7
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
hi i try to work with prokka to analize some genomes but i have this error :
Error executing process > 'roary'
Caused by: Missing output file(s)
roary/accessory_binary_genes.fa.newickexpected by processroaryCommand executed:
roary -e -n -t 11 -p 8 -f roary -i 95 -cd 99 Mars-10.bin.107.gff Mars-3.bin.148.gff
Command exit status: 0
Command output:
Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, MSG: G"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Use ofPubmed: 26198102
Command error: Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.28/Encode.pm line 69. Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl/5.28/Encode.pm line 69. Use of uninitialized value in require at (eval 1243) line 1. 2023/01/31 16:43:06 Input file to MAFFT missing: pan_genome_sequences/group_6.fa 2023/01/31 16:43:06 Input file to MAFFT missing: pan_genome_sequences/group_6.fa cat: pan_genome_sequences/group_6.fa: No such file or directory
--------------------- WARNING --------------------- MSG: Got a sequence without letters. Could not guess alphabet
--------------------- WARNING --------------------- MSG: Got a sequence without letters. Could not guess alphabet
Use of uninitialized value $gene_length in addition (+) at /usr/share/perl5/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm line 36.
Work dir: /mnt/c/users/giese/documents/ubuntu/ciano_anta/work/66/c30290a91d09b2837a65a7dd2a6fa7
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named
.command.sh