<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Wally<div><br></div><div>That’s quite an old release of Ensembl (June 2011), and we’ve made a lot of improvements to our code since then, so I would definitely recommend upgrading to a more recent version before looking further into this problem.</div><div><br></div><div>Regards</div><div><br></div><div>Anne</div><div><br></div><div><br></div><div><div>Anne Lyle</div><div>Ensembl Web Developer</div><div>European Bioinformatics Institute</div></div><div><br><div><div>On 22 Apr 2014, at 10:25, Jian-Ying Chiu <<a href="mailto:jychiu@ym.edu.tw">jychiu@ym.edu.tw</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I got an error when I was trying to upload a BAM file to our local</div>
<div style="font-family:arial,sans-serif;font-size:13px">bacteria ensembl genome browser (version 63). </div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
[Error from error_log]========================</div><div style="font-family:arial,sans-serif;font-size:13px"><a href="http://.../AN077_AYE_rmdup_rename_sorted.bam">http://.../AN077_AYE_rmdup_rename_sorted.bam</a> open: <span style="color:rgb(221,75,57);line-height:18.200000762939453px">bad file descriptor</span> at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 113.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><p>Failed to open BAM <a href="http://.../AN077_AYE_rmdup_rename_sorted.bam">http://.../AN077_AYE_rmdup_rename_sorted.bam</a> at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 123.</p><p>Failed to open BAM index for <a href="http://.../AN077_AYE_rmdup_rename_sorted.bam">http://.../AN077_AYE_rmdup_rename_sorted.bam</a> at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 124.</p><p>=======================================</p><p>I am very sure that the .bai file was put in the same dir. with BAM file.</p><p>And also, I can open this BAM file in command line. Does anyone know</p><p>where the problem is? </p><p>Should I upgrade our webcode to newer version for this issue? Besides,</p><p>which version of samtools and Bio::samtools should I use?</p><p><br></p><p>All the Best,</p><p>Wally Chiu </p></div><br clear="all"><div><br>
</div>-- <br><div dir="ltr">======================<br>Jian-Ying Chiu, R.A.<br>Institute of Biomedical Informatics<br>National Yang-Ming University<br>Taipei, Taiwan<br>Tel: <a value="+886228267000" style="color:rgb(17,85,204)">+886-2-28267000 ext 7359</a><br>
======================<br></div></div>
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