Question: [Fwd: Re: Error Occurred When Converting The Solid Output To Fastq]
0
Anton Nekrutenko ♦ 1.7k wrote:
Subject: Re: [galaxy-user] error occurred when converting the SOLID
output
to fastq
Date: Wed, June 8, 2011 5:48 pm
To: "Anton Nekrutenko" <anton@bx.psu.edu>
Dear Anton,
Thank you very much! I re-uploaded the input file this Monday and
galaxy
now can work well with the data. I guess the corrupted input file is
due
to some problem when I uploaded them via FTP software at the first
time.
:)
Best regards,
Sincerely,
Jia-Xing
--
Jia-Xing Yue
Graduate Student
Putnam Lab
Ecology & Evolutionary Bio. -MS 170
Rice University
6100 Main Street
Houston TX 77005
Phone: 1-832-360-6228
E-mail: yjx@rice.edu
Blog: http://bestrok.blogspot.com/
Specifically, you _F3 files are out of sync. One of the reads in
csfasta
file:
30 29 32 22 32 32 31 31 26 33 32 30 30 30 28 26 28 28 28 33 25 24 31
13
30 21 7 14 30
30 29 32 22 32 32 31 31 26 33 32 30 30 30 28 26 28 28 28 33 25 24 31
13
30 21 7 14 30
converted into fastq without explicit identifier matching. Please,
check
that your input csfasta and QUAL files have exactly the same number of
non-comment lines.
complained the following error. Does anybody know why>>
"/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq
.py",
line 207, in <module>
"/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq
.py",
line 188, in main
"/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq
.py",
line 207, in
"/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq
.py",
line 188, in main
double_encode=options.de, trim_first_base=options.trim_first_base,
min_qual=options.min_qual, table_name="f3" )
"/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq
.py",
line 83, in merge_reads_qual
defline, lines[0], qual ) )