BFAST - DATA SoLID

[jeferson]

can someone help with this error.

$ bfast-0.6.2a/bfast/bfast match -f reference/human/hg18.fa -A 1 -r reads.1.fastq > bfast.matches.file.hg18.1.bmf
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName reference/human/hg18.fa.
Validating readsFileName reads.1.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: reference/human/hg18.fa
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: reads.1.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 10000
tmpDir: ./
timing: [Not Using]
************************************************************
Searching for main indexes...
************************************************************
In function "GetIndexFileNames": Fatal Error[OutOfRange]. Variable/Value: reference/human/hg18.fa.cs.
Message: Could not find any indexes with the given prefix.
***** Exiting due to errors *****
************************************************************

[jeferson]

sorry. I rolled the problem.

$bfast-0.6.2a/bfast/bfast fasta2brg -f reference/human/hg18.fa

[jeferson]

sorry. I rolled the problem.

[jeferson]

Thank you for answering the topic before. run !

But I have a new problem.
which the error?

$bfast-0.6.2a/bfast fasta2brg -f reference/human/hg18.fa
-bash: bfast-0.6.2a/bfast: not directory

[westerman]

The error message does describe exactly what is wrong in my opinion. Namely that the read named "> 9_42_916_F3" from the CSFASTA file does not match the read named "> 9_42_20_F3 " in the corresponding QUAL file. I am a bit confused at what more information is required.

Ah, I read too fast after a several day hiatus from SeqAnswers and was only focusing in on the parts between the stars thinking for some reason that the starred part was the only important information. Probably if I was actually staring at the message on the screen instead of staring at it on a web page then the part of the message that told me the names of the sequences would jump out.

My apologies Nils. I should have known that you would write useful messages.


However going back to the original poster -- jeferson -- I wonder why he/she could not figure out what was the cause of the problem? If I were to guess it may because of the use of the term:

read-> name! = Qual_name

While the lines above that message talk about

0csfasta_name and qual_name

Which might, to some people, not mean the same as 'read' and 'Qual_name'. Furthermore the use of '! =' might not mean, to some people, 'not equal' and even if it means 'not equal' to them it might not come across to them that the two files need to have the same read names in them.

OTOH, writing error messages so that they are understandable to a wide range of people is difficult. In bioinformatics and especially 2ndgen bioinformatics we should assume that we are dealing with intelligent people who can figure out problems given enough information.

Anyway, enough rambling. Nils: your error message is fine.

[nilshomer]

Nils:

This touches on one of my 'hot topics' in error message -- the lack of enough information for the end user to figure out what is exactly wrong. Maybe you can change the program so that it outputs what read names are not matching. That would help in determining what is going wrong. Example:

Message: Read names did not match: 'read xyz' versus 'readABC'

The error message does describe exactly what is wrong in my opinion. Namely that the read named "> 9_42_916_F3" from the CSFASTA file does not match the read named "> 9_42_20_F3 " in the corresponding QUAL file. I am a bit confused at what more information is required.

Perhaps like this...?

Outputting, currently on:
0csfasta_name = [> 9_42_916_F3]
qual_name = [> 9_42_20_F3]

But why not just skip reads if names don't match?

Since the assumption is that each read in the CSFASTA is present in the QUAL file in the same order. If the files are corrupt etc. then this it is appropriate to abort. I prefer to be conservative in this case.

[Chipper]

Perhaps like this...?

Outputting, currently on:
0csfasta_name = [> 9_42_916_F3]
qual_name = [> 9_42_20_F3]

But why not just skip reads if names don't match?

[westerman]

Nils:

This touches on one of my 'hot topics' in error message -- the lack of enough information for the end user to figure out what is exactly wrong. Maybe you can change the program so that it outputs what read names are not matching. That would help in determining what is going wrong. Example:

Message: Read names did not match: 'read xyz' versus 'readABC'

[nilshomer]

when I run the script solid2fastq with the following command:

$ bfast-0.6.1c/scripts/solid2fastq n-10000000 reads barcode2/barcode2_F3.csfasta barcode2/barcode2_F3.qual

Surgi this error message:

Outputting, currently on:
0csfasta_name = [> 9_42_916_F3]
qual_name = [> 9_42_20_F3]
************************************************** **********
In function "fastq_read" Fatal Error [outofrange]. Variable / Value: read-> name! = Qual_name.
Message: Read names did not match.
***** Exiting due to errors *****
************************************************** **********

What would it be?

The reads in the CSFASTA should be in the same order as the QUAL file, which is not the case above. Have you manipulated the files prior to using "solid2fastq"? I see that you are barcoding, does that pre-process the CSFASTA/QUAL files?

Nils

[jeferson]

when I run the script solid2fastq with the following command:

$ bfast-0.6.1c/scripts/solid2fastq n-10000000 reads barcode2/barcode2_F3.csfasta barcode2/barcode2_F3.qual

Surgi this error message:

Outputting, currently on:
0csfasta_name = [> 9_42_916_F3]
qual_name = [> 9_42_20_F3]
************************************************** **********
In function "fastq_read" Fatal Error [outofrange]. Variable / Value: read-> name! = Qual_name.
Message: Read names did not match.
***** Exiting due to errors *****
************************************************** **********

What would it be?