I just tried via command line and re-did the steps that Galaxy attempted on the 
same files.  I got through the samtools sorting of the bam file without a 
problem, but then soon saw the same error when I tried executing freebayes 
itself:

[perin@variome 000]$ freebayes --fasta-reference 
/share/apps/genome/human/bwa/GRCh37_c/human_g1k_v37.fasta 
130_053_1.bwa-sorted.bam --vcf 130_053_1.freebayes.vcf -T 0.001 -p 2 -n 2 -M 
100 -m 10 -q 5 -x 0 -V 1.0 -W 2 -F 0 -C 1 -G 1 --min-coverage 0
BGZF ERROR: unable to open file 1.0
BGZF ERROR: unable to open file 1.0
Could not open input BAM files

My first guess is that the syntax for freebayes is wrong.  somewhere still.  
Because when i run without any flags, and simply try:

freebayes --fasta-reference 
/share/apps/genome/human/bwa/GRCh37_c/human_g1k_v37.fasta 
130_053_1.bwa-sorted.bam --vcf 130_053_1.freebayes.vcf

It seems to run.  I'm waiting for it to finish to verify.  However, i'm not 
sure if the default settings are adequate.  Moreover, I'm running this on Solid 
data (50bp fragment data) aligned by BWA after csfasta/qual to fastq conversion 
via galaxy.  I know initially freebayes was geared towards 454 data, but assume 
its find with any BAM file.  In any case, other than further editing the .xml 
file to omit flags, i'm not sure how else to 

NOTE.  I just tried one more thing.  i added a flag prior to the bam file name. 
 "-c" which is supposed to Read BAM input on stdin.  It now runs, but throws an 
error because of the input format.  So maybe this is a freebayes bug??

[perin@variome 000]$ freebayes --fasta-reference 
/share/apps/genome/human/bwa/GRCh37_c/human_g1k_v37.fasta --vcf 
130_053_1.freebayes.vcf -T 0.001 -p 2 -n 2 -M 100 -m 10 -q 5 -x 0 -V 1.0 -W 2 
-F 0 -C 1 -G 1 --min-coverage 0 --stdin 130_053_1.bwa-sorted.bam
--stdin flag specified, but a list of BAM files given.  Jumping disabled.

(...running now)

Juan



On Apr 5, 2011, at 8:56 AM, Dannon Baker wrote:

> Juan,
> 
> I'm not sure of a likely cause of this error off the top of my head.  Have 
> you tried running Freebayes from the command line on the same data input?  
> That might be an easy way to explore what particular options with the newer 
> version of Freebayes that you have are causing issues, or perhaps would let 
> us know if the input files are somehow truly invalid.
> 
> -Dannon
> 
> 
> On Apr 4, 2011, at 11:25 AM, Juan Carlos Perin wrote:
> 
>> This fix got me further, however I'm now getting the following error, which 
>> is now more confusing...
>> 
>> [bam_sort_core] merging from 40 files...
>> BGZF ERROR: unable to open file 1.0
>> BGZF ERROR: unable to open file 1.0
>> Could not open input BAM files
>> 
>> 
>> Juan
>> 
>> On Apr 1, 2011, at 1:53 PM, Dannon Baker wrote:
>> 
>>> Juan,
>>> 
>>> What version of freebayes are you running?  The freebayes configuration in 
>>> the galaxy repository was written with the .4 series in mind, and it 
>>> appears that the options have changed with the .6 series.  We'll update the 
>>> tool config, but in the meanwhile you could probably get it working again 
>>> for your local use by editing the 
>>> tools/human_genome_variation/freebayes.xml file to comment out the 
>>> no-longer-valid parameter in line 34:
>>> 
>>> -Y $params.postIntegBanddepth
>>> 
>>> 
>>> Let me know if this doesn't get things moving again for you,
>>> 
>>> Dannon
>>> 
>>> 
>>> On Apr 1, 2011, at 1:17 PM, Juan Carlos Perin wrote:
>>> 
>>>> I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment 
>>>> of solid data.  I keep getting the following error:
>>>> 
>>>> [bam_sort_core] merging from 40 files...
>>>> freebayes: invalid option -- Y
>>>> did you mean --bam ?
>>>> 
>>>> 
>>>> I'm not sure where this is set in the code to try to debug things.  I'm 
>>>> wondering if anyones had this error, and how to fix it?  Just to note, I'm 
>>>> running Brad Chapmans branch of galaxy for the LIMS functionality.  But it 
>>>> appears to be an issue with either galaxy-dist or this one. 
>>>> 
>>>> Thanks in advance for any advice. 
>>>> 
>>>> Juan Perin
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>>> 
>> 
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