Question: Error: Eof Marker Is Absent When Processing A Bam File
4
gravatar for Mary
8.4 years ago by
Mary40
Mary40 wrote:

Hi

I work with HAPCUT software to make Haplotypes using a sorted bam file and a vcf file containing varients. when i run this command ,

./extract_hairs --VCF variantfile.VCF --bam alignedreads.sorted.bam --maxIS 600 > fragment_matrix_file

an error says that

[bam_header_read] EOF marker is absent

also before that, when i tried to sort bam file with samtool this error occurred. but samtool continued to make sorted bam and then i used it in HAPCUT.

thanks for any advice on this problem.

samtools error • 9.7k views
ADD COMMENTlink modified 7.2 years ago by Istvan Albert ♦♦ 86k • written 8.4 years ago by Mary40

HAPCUT is interesting. How long are the haplotypes it generates from paired-end sequencing data?

ADD REPLYlink written 7.2 years ago by Erik Garrison2.3k
2
gravatar for Istvan Albert
8.4 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

You have an invalid bamfile. Recreate it.

ADD COMMENTlink written 8.4 years ago by Istvan Albert ♦♦ 86k

But I download my bamfile from this link: "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data" I think that problem is from other thing. I work with some variant somtool to create sorted file for using in HAPCUT, but error occurred every time.Is it possible that samtool do not work correctly? or my error is from other thing? thanks,

ADD REPLYlink modified 8.4 years ago • written 8.4 years ago by Mary40
1

If samtools raises an error then it means that your bamfile is incorrect. There are many ways a download can go bad, give us the link to the actual bamfile and perhaps someone can test it for you on their system.

ADD REPLYlink modified 8.4 years ago • written 8.4 years ago by Istvan Albert ♦♦ 86k

The actual link that i downloaded my bamfile is: " ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20111114.bam ".
I work on chromosome 11, if this error is from my file please tell me another link for download bamfile.

ADD REPLYlink modified 8.4 years ago • written 8.4 years ago by Mary40
2
gravatar for rob234king
7.2 years ago by
rob234king600
UK/Harpenden/Rothamsted Research
rob234king600 wrote:

If hard drive was full when made bam file it would stop but not give any indication so maybe the person that made the bam file did not notice that during the operation the hard drive became full. Try to get the sam file and convert yourself or use a different bam file to check it is the bam file which is not complete. I recently created a bam file but my hard drive was full so had this issue.

Even thought the file will be sorted using sam tools it is not the complete bam file so your results will not be based upon the full data set.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by rob234king600
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1858 users visited in the last hour
_