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Old 03-11-2011, 10:39 AM   #1
Morpse
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Location: Vancouver

Join Date: Mar 2011
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Default bcftools error

Hello,

The command
cat all.mpileup | bcftools view -bvcg - > all.var.raw.bcf

exits with the text below
[bcf_sync] incorrect number of fields (4 != 5) at 10:1696253
[afs] 0:38509.883 1:50.388 2:38.729

before exiting it outputs this text (this pattern starts at 100000)
[bcfview] 13600000 sites processed.
[afs] 0:99814.004 1:101.247 2:84.750
[bcfview] 13700000 sites processed.
[afs] 0:99786.086 1:107.189 2:106.725

all.mpileup was generated with the following command
samtools -verbose -uf reference.fasta all.bam > all.mpileup

Does anyone know what is causing this or how to fix it? I would like to be able to call both SNPs and indels with this.

Thank you

Last edited by Morpse; 03-11-2011 at 11:16 AM. Reason: typo
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Old 06-15-2011, 11:59 AM   #2
Hkins552
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Default Same problem

I am having the same problem, which is strange as I've used this exact pipeline/command previously with no issues. Have you figured anything out?
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Old 06-15-2011, 12:08 PM   #3
swbarnes2
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Default

The "incorrect number of files" can happen if the file is truncated. I see it sometimes if I want to check on a big files while it's still being made by mpileup.

What's the purpose of the cat command, and the pipe?
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Old 12-15-2011, 10:03 AM   #4
Mark.hz
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Default

I ran into the same problem, either with or without nohup. Does anyone know how to fix? Now I am generating the raw bcf file and try to figure out what is wrong on that specific line.
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Old 12-27-2011, 03:21 PM   #5
Mark.hz
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Default

Still have this problem when doing bcftools view for a bcf file (mpileup generated): [bcf_sync] incorrect number of fields (6 != 5) at 7:1396330564
Any help?
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Old 10-05-2012, 01:05 AM   #6
figo1019
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Default

Quote:
Originally Posted by Mark.hz View Post
Still have this problem when doing bcftools view for a bcf file (mpileup generated): [bcf_sync] incorrect number of fields (6 != 5) at 7:1396330564
Any help?
Hi Mark.hz

Have you sorted out this problem as I am also facing the similar error while running the bcf file [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867.

Regards
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Old 10-05-2012, 10:01 AM   #7
Mark.hz
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Default

Quote:
Originally Posted by figo1019 View Post
Hi Mark.hz

Have you sorted out this problem as I am also facing the similar error while running the bcf file [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867.

Regards
Truncated BAM file may cause this problem. You need to go back to validate your BAM files by Picard.
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Old 10-05-2012, 11:51 AM   #8
figo1019
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Quote:
Originally Posted by Mark.hz View Post
Truncated BAM file may cause this problem. You need to go back to validate your BAM files by Picard.
Thank you for your reply

I ran the picard tool to validate I get an error
ERROR: Read groups is empty

Rest things are OK.

Does it make a huge difference ?

regards
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Old 10-05-2012, 12:24 PM   #9
Mark.hz
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Quote:
Originally Posted by figo1019 View Post
Thank you for your reply

I ran the picard tool to validate I get an error
ERROR: Read groups is empty

Rest things are OK.

Does it make a huge difference ?

regards
Strange. I don't think RG is the reason. Did the validation stop at the 1st error?
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