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Old 10-07-2011, 05:15 AM   #1
CS Student
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Default BFAST- specifying tmpDir parameters

Hi,

I am trying to use the (-T) option in the bfast "match" command to specify the directory to which temporary files will be written instead of the default directory (current directory), but not yet able to do so!

I am trying to use the following command:
bfast match -f phi.x.174.fa -r reads.phi.x.174.fastq -T '/home/student/bfast/tmpDir' > bfast.matches.file.phi.x.174.bmf

and I get this error:
In function "BfastMatchValidateInputs": Fatal Error[IllegalPath]. Variable/Value: tmpDir.
Message: Command line argument.
***** Exiting due to errors *****

Could anyone please advise on how to specify the "path" in the (-T) option?

Thanks in advance.
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Old 10-07-2011, 05:52 PM   #2
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Get rid of the apostrophes.
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Old 10-07-2011, 11:28 PM   #3
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I tried removing the apostrophes, but still getting the same error!

Could you please advise on another solution?

Thanks.
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Old 10-08-2011, 12:01 AM   #4
Michael.James.Clark
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Fix the path to your tmpDir. It's wrong if you're getting that error.

Just did this today with "-T tmp/" and it worked fine.
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Old 10-08-2011, 10:06 AM   #5
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Thanks Michael.

I tried with double quotations as you did and added the "/" character at the end of my path and it worked.

I have another problem now. I get the following error [at the end of the code below]:

Checking input parameters supplied by the user ...
Validating fastaFileName phi.x.174.fa.
Validating readsFileName reads.phi.x.174.fastq.
Validating tmpDir path home/student/bfast-0.6.4f/output/.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: phi.x.174.fa
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: reads.phi.x.174.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: home/student/bfast-0.6.4f/output/
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 5 index (5 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from phi.x.174.fa.nt.brg.
In total read 1 contigs for a total of 5386 bases
************************************************************
Reading reads.phi.x.174.fastq into a temp file.
************************************************************
In function "OpenTmpGZFile": Fatal Error[IllegalFileName]. Variable/Value: home/student/bfast-0.6.4f/output/.bfast.tmp.5OL5Ka.
Message: Could not create a tmp file name.
***** Exiting due to errors *****


Any suggestions?

Thanks.
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Old 10-09-2011, 01:38 PM   #6
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home/student/bfast-0.6.4f/output should be /home/student/bfast-0.6.4f/output (leading slash!)
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Old 10-09-2013, 10:48 AM   #7
stqa8350
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Hello,

I have the same problem and I am unable to solve them. Checking through various threads, I have done all that I can

1. Make install bfast from github

2. Re-indexed reference file with depth '0'

And the script used is the following;
bsub -I /tools/bfast/bfast/bfast match -A 1 -t -n 8 -f /solid-v2/Homo_sapiens_assembly19.fasta -T $HOME/tmp/ -r /data/fastq/test.fastq > test.matches.bmf

The Error is:

Validating tmpDir path /PHShome/us024/tmp/*.
************************************************************
In function "BfastMatchValidateInputs": Fatal Error[IllegalPath]. Variable/Value: tmpDir.
Message: Command line argument.
***** Exiting due to errors *****

Any suggestion to resolve this will be very helpful. The tmp dir is my home dir will the requisite permissions.

Many thanks

Uma
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