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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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error message #4

Closed CCgenetics15 closed 6 years ago

CCgenetics15 commented 9 years ago

Hi, I'm trying to use ExomeDepth but I have the following error message:

my.counts <- getBamCounts(bed.frame = exons.hg19,bam.files= sample1.bam, include.chr=TRUE) Parse 1 BAM files [1] "sample1.bam" Now parsing sample1.bam [bam_header_read] EOF marker is absent. The input is probably truncated. Parsing chromosome chr1 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_index_load] fail to load BAM index. Error in value[3L] : failed to open BamFile: failed to load BAM index file:sample1.bam Inoltre: Warning messages: 1: 'isNotPrimaryRead' is deprecated. Use 'isSecondaryAlignment' instead. See help("Deprecated") 2: 'isNotPrimaryRead' is deprecated. Use 'isSecondaryAlignment' instead. See help("Deprecated")

help("Deprecated") Can you help me? Thanks

vplagnol commented 9 years ago

Can you try exomeDepth version 1.1.6 please, just pushed to CRAN last night? But besides that it looks like there is something wrong with your BAM file, based on the error message.

On Thu, Sep 3, 2015 at 8:22 AM, CCgenetics15 notifications@github.com wrote:

Hi, I'm trying to use ExomeDepth but I have the following error message:

my.counts <- getBamCounts(bed.frame = exons.hg19,bam.files= sample1.bam, include.chr=TRUE) Parse 1 BAM files [1] "sample1.bam" Now parsing sample1.bam [bam_header_read] EOF marker is absent. The input is probably truncated. Parsing chromosome chr1 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_index_load] fail to load BAM index. Error in value[3L] http://cond : failed to open BamFile: failed to load BAM index file:sample1.bam Inoltre: Warning messages: 1: 'isNotPrimaryRead' is deprecated. Use 'isSecondaryAlignment' instead. See help("Deprecated") 2: 'isNotPrimaryRead' is deprecated. Use 'isSecondaryAlignment' instead. See help("Deprecated")

help("Deprecated") Can you help me? Thanks

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/ExomeDepth/issues/4.

Vincent Plagnol University College London Genetics Institute Darwin building, office 210 Gower Street, London, WC1E 6BT Cell: +44-(0)7946-546923 Office: +44-(0) 2031-084002 Website: http://www.ucl.ac.uk/ugi/research/vincentplagnol Lab blog: http://plagnol-lab.blogspot.co.uk/

CCgenetics15 commented 9 years ago

Hi Vincent, I tried the last version of ExomeDepth. I had the same error. I used another bam file and the program worked without problems. So now I don't know what goes wrong with the first bam file. Do you have any suggestion? Thanks for your help

vplagnol commented 6 years ago

This is a very old issue, I presume not relevant anymore and I will close.