Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Same here, the bcftools that is compiled within samtools is old, and when I compiled a fresh version from github, this error vanished.
-
hello,all,I think I have solve this problem:
both nohup and ">" would add stdout and stderr to output file,which cause that problem。
so,
"samtools mpileup -ugf F.fna F.sorted.bam -o F.bcf"
instead of
"samtools mpileup -ugf F.fna F.sorted.bam > F.bcf"
Leave a comment:
-
I got the same problem. I tried the verson 1.0, 0.1.19, 0.1.18 and none worked.
Any one can help to solve this problem.
Here are my command and error message:
samtools mpileup -ugf F.fna F.sorted.bam > F.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bcf_sync] incorrect number of fields (6 != 5) at 67:234
Segmentation fault
Leave a comment:
-
I had the same problem. I think the problen is that bcftools works with bcf-file but you don't specify for samtools to output bcf. So you should add to samtools mpileup command argument -g.
Hope this was helpful.
Leave a comment:
-
I'm getting this error with this command
samtools mpileup -D -S -u -f hg19.fasta child.bam father.bam mother.bam | bcftools view -vcgT trioauto -s sample.txt - > samtoolsCLR.vcf
The resulting vcf file just has the INFO and FORMAT ## lines, then:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs] 0:0.000
I am using the correct fa reference file.
My samples file looks like:
child.bam
father.bam
mother.bam
Any advice appreciated.
Leave a comment:
-
The problem occurs when nohup is used with a Unix pipe.
I've just sent this reply to the samtools-help mailing list.
nohup merges stdout and stderr of the command that it runs. bcftools then
doesn't know what to do with the input data since it also contains messages
such as "[mpileup] 1 samples in 1 input files".
To avoid the problem, you can run the command like this:
nohup samtools mpileup ... 2> stderr.txt | bcftools ... - > out.raw.bcf &
But I strongly suggest you try the 'screen' program. It is less fragile and
much more powerful than nohup. This is the briefest introduction I could find: http://www.askbjoernhansen.com/2006/...ix_screen.html
Leave a comment:
-
I also had the problem when using nohup. Without nohup. it goes well.
Leave a comment:
-
Make sure you're using the correct reference genome
In case anyone else encounters this same problem ("[bcf_sync] incorrect number of fields (6 != 5)..."), here's another possible solution:
I was having this problem with multiple files, but then I realized I was using the wrong reference fasta as the argument to the mpileup -f option. It wasn't the same reference fasta that was used to create the bam files. When I switched to the correct one, the problem went away.
Leave a comment:
-
I still got the error message without nohup: "[bcf_sync] incorrect number of fields (6 != 5) at 7:1396330564"
Leave a comment:
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Leave a comment: