Question: peak calling in MACS2
0
gravatar for mohamed_ismail
3.0 years ago by
United States
mohamed_ismail10 wrote:

I am trying to do peak calling of paired-end sequences using MACS2 in Galaxy. The Filter SAM files shows the Error message:  [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!

subsequently, the following peak calling files are paused and do not run further. 

48: MACS2: callpeak on data 47 and data 45 (peaks: bed)

49: MACS2: callpeak on data 47 and data 45 (html report)

50: MACS2: callpeak on data 47 and data 45 (peaks: xls)

51: MACS2: callpeak on data 47 and data 45 (peaks: encodePeak)

52: MACS2: callpeak on data 47 and data 45 (peaks: interval)

53: MACS2: callpeak on data 47 and data 45 (negative peaks: interval)

 

Please help me to fix this problem

galaxy • 2.0k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by mohamed_ismail10
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The  issue is with the tool "Filter SAM on bitwise flag values"? Examine the input and adjust it so that it is in specification. Meaning, the SAM dataset should have headers. There is a tool in the Picard tool group that will add this back in if missing. The other message about the file being truncated is likely not the root cause of the problem.

Many tools are specific and input format problems are the #1 cause of job errors. This section of the Galaxy wiki has a fairly comprehensive list of troubleshooting help for the most common types of input/configuration issues encountered with probable solutions.
http://wiki.galaxyproject.org/Support Section 2.8.1

Best, Jen, Galaxy team

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson24k

Thanks Very much


From: Jennifer Hillman Jackson on Galaxy Biostar [notifications@biostars.org] Sent: Friday, May 08, 2015 9:34 AM To: Ismail, Mohamed Subject: [galaxy-biostar] A: peak calling in MACS2

Activity on a post you are following on Galaxy Biostar<http: biostar.usegalaxy.org="">

User Jennifer Hillman Jackson<http: biostar.usegalaxy.org="" u="" 254=""/> wrote Answer: peak calling in MACS2<http: biostar.usegalaxy.org="" p="" 12098="" #12113="">:

Hello,

The issue is with the tool "Filter SAM on bitwise flag values"? Examine the input and adjust it so that it is in specification. Meaning, the SAM dataset should have headers. There is a tool in the Picard tool group that will add this back in if missing. The other message about the file being truncation is likely not the root cause of the problem.

Many tools are specific and input format problems are the #1 cause of job errors. This section of the Galaxy wiki has a fairly comprehensive list of troubleshooting help for the most common types of input/configuration issues encountered with probable solutions. http://wiki.galaxyproject.org/Support Section 2.8.1

Best, Jen, Galaxy team

ADD REPLYlink written 3.0 years ago by mohamed_ismail10
0
gravatar for mohamed_ismail
3.0 years ago by
United States
mohamed_ismail10 wrote:

Hi Jennifer,

The Filter SAM dataset has QNAME for each flag values. I assume this is what you are referring as headers. However, I continued to fix this using Picard tool>Replace SAM/BAM header. Unfortunately, I end up with errors again.

In Replace SAM/BAM header, what is the source file that should be uploaded? I used varying source files of the target source but could not fix it. 

I didn't have this issue when I used previous MACS version for single end peak calling. I could not figure out this issue in the support tool you had suggested. Please let me know what I am missing?

 

ADD COMMENTlink written 3.0 years ago by mohamed_ismail10
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