SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie2-build error writing to reference index file cz0013 Bioinformatics 8 08-17-2015 09:31 AM
Samtools Segmentation error while using samtools index AnushaC Bioinformatics 3 06-18-2014 07:01 AM
HTSeq.BAM_Reader error: .bam-file has no index ... JIrish Bioinformatics 4 10-09-2013 09:35 AM
samtools sort bam file error: generate non-existent file mediator Bioinformatics 0 03-05-2012 08:42 PM
Local Blast Error of index file Shani Bioinformatics 0 02-12-2011 01:45 AM

Reply
 
Thread Tools
Old 02-19-2019, 09:59 AM   #1
NDUFB11
Member
 
Location: Italy

Join Date: Jul 2017
Posts: 27
Default samtools index file error

Hello,

I have to post process the outcome STAR file .bam but when I go to create an index for it I have an error with samtools,


Code:
Patrizios-MBP:star patrizio$ samtools index SRR359063.bam
dyld: Symbol not found: _stdscr
  Referenced from: /Users/patrizio/anaconda3/bin/samtools
  Expected in: /Users/patrizio/anaconda3/bin/../lib/libncursesw.6.dylib
 in /Users/patrizio/anaconda3/bin/samtools
Abort trap: 6

I read online and seems to be related with anaconda but I don't know how to fix it, anyone experienced that?

thank you


-P
NDUFB11 is offline   Reply With Quote
Old 02-19-2019, 10:15 AM   #2
NDUFB11
Member
 
Location: Italy

Join Date: Jul 2017
Posts: 27
Default

ok probably I solved the problem by using this line command to install a older version of samtools

conda install -c bioconda samtools=1.9=h8ee4bcc_1


from this forum discussion


https://github.com/bioconda/bioconda...s/issues/13488
NDUFB11 is offline   Reply With Quote
Old 02-19-2019, 11:48 AM   #3
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,881
Default

Samtools 1.9 is the latest version.
GenoMax is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:44 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO