peak calling in MACS2

Question: peak calling in MACS2

3.6 years ago by

United States

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

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modified 3.6 years ago • written 3.6 years ago by mohamed_ismail • 10

3.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

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,

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 REPLY • link written 3.6 years ago by mohamed_ismail • 10

3.6 years ago by

mohamed_ismail • 10

United States

mohamed_ismail • 10 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 COMMENT • link written 3.6 years ago by mohamed_ismail • 10

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