paparazzi

[giampe]

dear all,
anyone of you have used this software (Paparazzi) to reconstruct viral genome from short reads?
I have this message coming out when I try to run it:

[user1@netlab01:~/data_from_testuser1/paparazzi_new_version]$ paparazzi ./paparazzi_conf_file.txt
P1B_clipped GPGV
Creating target directories
Filtering host-derived reads
Could not locate a Bowtie index corresponding to basename "path_to_reference_genome_bowtie_library_including_library_basename"
Command: bowtie -v 0 --threads 4 --solexa-quals --quiet --un ../filtered/P1B_clipped_unmatched.fq path_to_reference_genome_bowtie_library_including_library_basename /home/user1/data_from_testuser1/LIBRERIE_OTTOBRE/P1B/P1B_clipped.fq
Died at /home/user1/bin/paparazzi line 80, <$fh> line 1.
thanks for help

[dariober]

Hi- I know nothing about Paparazzi but it looks like Bowtie cannot find the index file path_to_reference_genome_bowtie_library_including_library_basename

Are you sure "path_referenence..." is exactly the basename of the index? It looks more like the name of a variable or some comment string. Try posting also the content of ./paparazzi_conf_file.txt

Good luck!
Dario

[giampe]

hi Dario,
thanks for your reply, here http://carla.saleh.free.fr/software/paparazzi.html you can find the documentation of this software, about your suggestion the basename of my index is vitis and in the line 8 of the script I have already changed the path for the my host genome (vitis). The building of bowtie library by bowtie-build command it seems ok. I'm sending you also the paparazzi script so you can see if there is something wrong. I'm a poor biologist so I don't know if I did in exact way!
thanks

[dariober]

Hi- In the script you sent the reference genome seems to be on line 8

$reference_host_lib = '/home/user1/data_from_testuser1/paparazzi_new_version/bowtie_lib/vitis/vitis.';

While the is no string matching "path_to_reference_genome_bowtie_library_including_library_basename"

If anything, paparazzi/bowtie should complain about not finding /home/user1/data_from_testuser1/paparazzi_new_version/bowtie_lib/vitis/vitis.

Are you sure this is the script that generated the error you posted?

EDIT:

I think you are running the script dowloaded from http://carla.saleh.free.fr/software/paparazzi where indeed there is on line 8 $reference_host_lib = 'path_to_reference_genome_bowtie_library_including_library_basename';

[giampe]

hi,
you are right but if you take a look at the documentation file of paparazzi(point 3-Installation) you can see that they indicate to change in the script line 8 entering "the absolute path for the host genome bowtie library, including the basename"