Question: Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
0
gravatar for Lisanne
6.1 years ago by
Lisanne0
Lisanne0 wrote:

Dear All,

Today I downloaded MACS. MACS is a program to analyze chip-seq data. The installation was complete and without errors. Now I want to use MACS in the command line (Iam using Linux) and a get an zlib error. Could someone tell me what it means?

lisanne@t77:~/MACS> macs14 -t /home/lvijfhuizen/ES-OBX_chip_1_CGATGT_1494_R106L8_AA-uq37.bam -n aap
INFO  @ Wed, 14 Sep 2011 15:38:33:

# ARGUMENTS LIST:
# name = aap
# format = AUTO
# ChIP-seq file = /home/lvijfhuizen/ES-OBX_chip_1_CGATGT_1494_R106L8_AA-uq37.bam
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = 10,30
# pvalue cutoff = 1.00e-05
# Small dataset will be scaled towards larger dataset.
# Range for calculating regional lambda is: 10000 bps

INFO  @ Wed, 14 Sep 2011 15:38:33: #1 read tag files...
INFO  @ Wed, 14 Sep 2011 15:38:33: #1 read treatment tags...
INFO  @ Wed, 14 Sep 2011 15:38:33: Detected format is: BAM
INFO  @ Wed, 14 Sep 2011 15:38:33: tag size: 50
Traceback (most recent call last):
File "/home/lvijfhuizen/Downloads/MACS/bin/macs14", line 358, in <module>
 main()
File "/home/lvijfhuizen/Downloads/MACS/bin/macs14", line 60, in main
 (treat, control) = load_tag_files_options (options)
File "/home/lvijfhuizen/Downloads/MACS/bin/macs14", line 330, in load_tag_files_options
 treat = tp.build_fwtrack()
File "/home/lvijfhuizen/Downloads/MACS/lib64/python2.6/site-packages/MACS14/IO/Parser.py", line 809, in build_fwtrack
entrylength = struct.unpack('<i', fread(4))[0]
File "/usr/lib64/python2.6/gzip.py", line 219, in read
self._read(readsize)
File "/usr/lib64/python2.6/gzip.py", line 271, in _read
uncompress = self.decompress.decompress(buf)
zlib.error: Error -3 while decompressing: invalid distance too far back

Could anyone help me with this error? Thank you!

error • 5.1k views
ADD COMMENTlink written 6.1 years ago by Lisanne0
1

Sounds like a decompression error. Check your BAM file, is it compressed and correct? Can you run a query on it? samtools view my.bam chr1:100-200

ADD REPLYlink written 6.1 years ago by Istvan Albert ♦♦ 74k
1

First I would make sure that it transferred correctly, run the query on the new computer, like I said it sounds like an input file error. The next step would be to convert your BAM files to SAM and use the -format SAM option in MACS to check whether the pipeline works as it should use: samtools view my.bam > my.sam

ADD REPLYlink written 6.1 years ago by Istvan Albert ♦♦ 74k
1

I agree. Sounds like a corrupt bam file.

ADD REPLYlink written 6.1 years ago by Sean Davis23k

Dear Istvan, The BAM file is correct because the file is running on an another pc.

ADD REPLYlink written 6.1 years ago by Lisanne0
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