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Old 11-23-2010, 04:56 AM   #1
michalkovac
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Location: Oxford

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Default Dindel crash whilst parsing bam-sorted file

Dear All,

Does have anyone idea what might have cause this crash?
Thanks.
Michal

-------
dindel --analysis getCIGARindels --bamFile ./Post_Assembly/Temp/2007.02142B.normal.merged.out.bam --outputFile normal.sorted.bam --ref ./Reference_Indexed/Human36
-------
Reading BAM file: ./Post_Assembly/Temp/2007.02142B.normal.merged.out.bam
Parsing indels from CIGAR strings...
Number of reads read: 1000000
Number of reads read: 2000000
Number of reads read: 3000000
Number of reads read: 4000000
Number of reads read: 5000000
Number of reads read: 6000000
Number of reads read: 7000000
Number of reads read: 8000000
Number of reads read: 9000000
Number of reads read: 10000000
Number of reads read: 11000000
Number of reads read: 12000000
Number of reads read: 13000000
Number of reads read: 14000000
Number of reads read: 15000000
Number of reads read: 16000000
Number of reads read: 17000000
Number of reads read: 18000000
error: faidx error, len==0
start: -88 end:
error: faidx error, len==0
start: -48 end:
error: faidx error, len==0
start: -4 end:

Last edited by michalkovac; 11-23-2010 at 07:28 AM.
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Old 11-23-2010, 06:40 AM   #2
zee
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It seems to be complaining about your faidx file. Check whether ./Reference_Indexed/Human36 is a fasta file and that ./Reference_Indexed/Human36.fai exists and it was made with "samtools faidx" or Picard.
It looks as though something is wrong with the reference sequence specified with --ref
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Old 11-23-2010, 07:12 AM   #3
michalkovac
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Reference file is ok and indexed with SAM tools. Or alternatively, dindel makes it's own fai when absent.
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Old 11-23-2010, 07:15 AM   #4
zee
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I am using dindel 1.01 and my command is

Code:
dindel --analysis getCIGARindels --bamFile  file.bam  --outputFile file.dindel --ref genome.fa
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Old 04-18-2011, 10:07 PM   #5
prokagenomics
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I get same problem...The output file, sample.dindel_output.variants.txt, is empty...
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Old 04-19-2011, 10:30 AM   #6
Michael.James.Clark
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Forum search reveals:

http://seqanswers.com/forums/showthr...%2C+len%3D%3D0
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Old 04-19-2011, 08:23 PM   #7
prokagenomics
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Default More information required

Thank you for the important URL.
in my Parsing indels from CIGAR strings...
"error: faidx error, len==0" appears more than 300,000 times.
And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
Is it normal? Actually I know my sequences have SNPs.
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Old 06-02-2011, 07:49 PM   #8
nb509
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Smile the same problem with you

Quote:
Originally Posted by prokagenomics View Post
Thank you for the important URL.
in my Parsing indels from CIGAR strings...
"error: faidx error, len==0" appears more than 300,000 times.
And in the output files (sample.dindel_output.libraries.txt, sample.dindel_output.variants.txt), sample.dindel_output.variants.txt is empty.
The URLs says "Also the faidx errors are apparently nothing to worry about.". So maybe other problem?
Not final vcf file but "sample.dindel_output.variants.txt" created at the stage 1 is empty. (of course, final vcf is also empty)
Is it normal? Actually I know my sequences have SNPs.
I have the same problem.
Many errors like this:
----------------
Wrote indels in CIGARS for target NR_027432:81795970-81828929 to file chr10.dindel_output2
error: faidx error, len==0
start: -20 end:
error: faidx error, len==0
start: -16 end:
error: faidx error, len==0
start: 1545 end:
error: faidx error, len==0
start: 2131 end:
error: faidx error, len==0
start: 2132 end:
error: faidx error, len==0
start: 1553 end:
error: faidx error, len==0
start: 1946 end:
error: faidx error, len==0
start: 633 end:
--------------------------------

and in the stage 1, the sample.dindel_output.variants.txt is empty.

Did you fix this?
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Old 02-16-2012, 06:56 PM   #9
jjinking
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Default Empty sample.dindel_output.variants.txt file

I'm having the same problem of empty sample.dindel_output.variants.txt file.
Here is is my command:

Code:
dindel-1.01-linux-64bit --analysis getCIGARindels \
                                --bamFile $bamfile \
                                --outputFile $bamfile.dindel \
                                --ref $REF &
dindel-1.01-linux-64bit is the linux binary that I downloaded from http://www.sanger.ac.uk/resources/software/dindel/

I also get error outputs like the following:

error: faidx error, len==0
start: 242960712 end:
error: faidx error, len==0
start: 145017722 end:
error: faidx error, len==0
start: 244903563 end:
...


Was anyone able to solve this problem?
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