Question: MACS2- struct.error: unpack requires a string argument of length 4
0
gravatar for 200dumplings
9 months ago by
200dumplings10
200dumplings10 wrote:
Command line: callpeak -t filtered_H3K9ME3_MEIS1_NATIVE_A10.bam -f BAM -c input_Meis1_native_D02.bam -g mm --broad --broad-cutoff 0.1

ARGUMENTS LIST:
name = NA
format = BAM
ChIP-seq file = ['filtered_H3K9ME3_MEIS1_NATIVE_A10.bam']
control file = ['input_Meis1_native_D02.bam']
effective genome size = 1.87e+09
band width = 300
model fold = [5, 50]
qvalue cutoff for narrow/strong regions = 5.00e-02
qvalue cutoff for broad/weak regions = 1.00e-01
The maximum gap between significant sites is assigned as the read length/tag size.
The minimum length of peaks is assigned as the predicted fragment length "d".
Larger dataset will be scaled towards smaller dataset.
Range for calculating regional lambda is: 1000 bps and 10000 bps
Broad region calling is on
Paired-End mode is off

INFO @ Wed, 08 May 2019 17:48:44: #1 read tag files...
INFO @ Wed, 08 May 2019 17:48:44: #1 read treatment tags...
INFO @ Wed, 08 May 2019 17:48:48: 1000000
INFO @ Wed, 08 May 2019 17:48:52: 2000000
INFO @ Wed, 08 May 2019 17:48:55: 3000000
(...)
INFO @ Wed, 08 May 2019 17:54:03: #1.2 read input tags...
Traceback (most recent call last):
File "/usr/local/bin/macs2", line 622, in 
main()
File "/usr/local/bin/macs2", line 57, in main
run( args )
File "/Library/Python/2.7/site-packages/MACS2/callpeak_cmd.py", line 73, in run
else: (treat, control) = load_tag_files_options (options)
File "/Library/Python/2.7/site-packages/MACS2/callpeak_cmd.py", line 411, in load_tag_files_options
control = options.parser(options.cfile[0], buffer_size=options.buffer_size).build_fwtrack()
File "MACS2/IO/Parser.pyx", line 876, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:13658)
File "MACS2/IO/Parser.pyx", line 889, in MACS2.IO.Parser.BAMParser.build_fwtrack (MACS2/IO/Parser.c:13066)
File "MACS2/IO/Parser.pyx", line 862, in MACS2.IO.Parser.BAMParser.get_references (MACS2/IO/Parser.c:12582)
struct.error: unpack requires a string argument of length 4

Wondering what went wrong in this command?

chip-seq macs2 • 654 views
ADD COMMENTlink modified 9 months ago by ATpoint29k • written 9 months ago by 200dumplings10

I added some highlighting to your post. Please use the code option(10101) from now on. I also shortened the log report a bit (deleted some lines after INFO @ Wed, 08 May 2019 17:48:55: 3000000and added (...) instead) to improve readability.

As for the question, what is the output of samtools quickcheck -qvvv input_Meis1_native_D02.bam and samtools view input_Meis1_native_D02.bam | head? It could be a problem with the control file.

ADD REPLYlink written 9 months ago by ATpoint29k

The output of samtools quickcheck -qvvv input_Meis1_native_D02.bam is: verbosity set to 3 checking input_Meis1_native_D02.bam opened input_Meis1_native_D02.bam input_Meis1_native_D02.bam is sequence data input_Meis1_native_D02.bam had no targets in header. input_Meis1_native_D02.bam cannot be checked for EOF block because its filetype does not contain one. input_Meis1_native_D02.bam

and the output of samtools view input_Meis1_native_D02.bam | head is silent.

Looks like you are right on! It is probably a problem with the control file. I was wondering though, what could have gone wrong? The upstream steps are: Illumina seq, alignment using bowtie2, blacklist removal using ENCODE .bed files in bedtools.

Thanks for the help!

ADD REPLYlink written 9 months ago by 200dumplings10

Also checked the control file, it turned out to be empty. I think maybe something happened when I was removing the blacklist regions?

ADD REPLYlink written 9 months ago by 200dumplings10

Command for removal?

ADD REPLYlink written 9 months ago by ATpoint29k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1526 users visited in the last hour