Let me know if these suggestions don't help.
Nathan
The script was written by Spencer--Spencer will you let Nathan know where the .sh file is?
Evan
Yes, I found the input file was not in the directory in the command. I
made a mistake. It works now. Also, it will be great if gnumap reports
"input sequence file does not exist in the directory or unknown
directory or file" for this case, Thanks, Nathan
Actually, the sample reads were captured from a big seq read file,
because a log file from the original experiment reports "Found error
...atteming to resolve...". Refer to [a1]
For a run command, refer to [a2]
I am wondering if this is related to some buffering option or do you
have any clue?
[a2]===============
Command Line Arguments:
/fslgroup/fslg_genome/software/gnumap_MPI/bin/gnumap -g
/fslhome/hongcj92/fsl_groups/fslg_maker/compute/bisulfite/genome/chr20.fa -o
/fslhome/hongcj92/fsl_groups/fslg_maker/compute/bisulfite/seqfiles/7795X1/gnumap/1_7_1
-p -a .9 -c 1 /fslhome/hongcj92
/fsl_groups/fslg_maker/compute/bisulfite/seqfiles/7795X1/7795X1_101213_SN141_0318_B80EE9ABXX_7_1.txt
-m 14 -j 25 -S /fslhome/hongcj92
/fsl_groups/fslg_maker/compute/bisulfite/scripts/pwm.CtoT -b -0 --illumina
[a1]===============
--Found error...atteming to resolve...
--ERROR at sequence
GGATGAAGGAAGAAAATTAGAGGAGAATTTAGTGTAGATAGAGAGAATCGATGAGGGGTTTTTTGAGTTATGAA
AATGTGAAAGAT (name[s] formatted incorrectly)
Trying to recover...
Reads per processor: 1024
--Found error...atteming to resolve...
--ERROR at sequence TGGGGGAAGTGGTAGGAGATGGGATTTGAGT (name[s] formatted
incorrectly)
Trying to recover...
Reads per processor: 1024
--Found error...atteming to resolve...
--ERROR at sequence 8:7:2:16003:26480#0/1 (name[s] formatted incorrectly)
Trying to recover...
Reads per processor: 1024
--Found error...atteming to resolve...
--ERROR at sequence
ggdcce_dbdda^cddddadbZebccebbcc`_]cadaX_aaS^ZaTa\X\aaS_]`bVZ_[ZUTTZV`]_`\a
daac^Z_cBBBBBBBBBBB (name[s] formatted incorrectly)
Trying to recover...
Reads per processor: 1024
--Found error...atteming to resolve...
--ERROR at sequence 141_0318:7:4:18131:146671#0/1 (name[s] formatted
incorrectly)
Trying to recover...
Reads per processor: 1024
===============
For your information, the specifications for fastq format can be found here: http://maq.sourceforge.net/fastq.shtml
Nathan
Is qseq the standard for Illumina data? If so, I'll implement it in GNUMAP.
In the meantime, here's a link to a Python script that can convert between the two. It's just a function and looks like it could be done much simpler, but I'll leave that to someone better with Python.
Nathan