Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)

Question

[Lisanne]

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!

[Istvan Albert]

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

[Istvan Albert]

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

[Sean Davis]

I agree. Sounds like a corrupt bam file.

[Lisanne]

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