"first magic byte doesn't match" error in FusionMap

Question

[noushin.farnoud]

Dear BioStars,

I am trying to run FusioMap to detect candidate fusions in a paired end RNASeq data set. I have already tested this dataset with a few other fusion algorithms and received no error (so am sure the .fastq files are not corrupted). But when running with FusionMap I get this error.

I hope you can help me understand what this error is actually referring to? and how I can resolve this?

Many thanks for your time in advance!

Noushin

​OShell version=8.0.2.32
Program started at Monday, November 16, 2015 12:37:32 PM
Perform initialization...

[00:00:00] Linux PDF library is used
[00:00:00] Linux OS detected...Initialization done...
TempFolder=/ifs/.../.../noushin/temp/FusionMapTemp/2015.11.16.b775cfda87e1d3d6
semap -- version 8.0.2.32

[00:00:02] Loading text information....
[00:00:02] Thread number=8
[00:00:02] Loading gene model........................................................................................................
[00:00:02] Submitting 1 OAlign jobs...
[00:00:02] Performing alignment for observation  RNAseq_SampleFusTestA...
[00:00:02] Calling /home/rahnaman/mono-2.10.9/bin/mono "/home/rahnaman/FusionMap_2015-03-31/bin/oalign.exe" RnaSeqG_Fusion "RNAseq_SampleFusTestA" "/home/rahnaman/App/FusionMap/ClusterScripts/Jobs/2015_11_16_160794be841bdb18.pi" "/home/rahnaman/App/FusionMap/Cluste
rScripts/Jobs/2015_11_16_160794be841bdb18.errorlog"
[00:00:02] Parent process ID is 31678
[00:00:03] Use .bim file for bam file indexing
[00:00:03] Running oalign.exe from computer: xxx.xxx.xxx.org...
[00:00:03] OSA version=4
[00:00:03] Loading gene model.......................................................................................................
[00:00:03] ThreadNumber was set to 8...
[00:00:03] Error occurred for job (RNAseq_SampleFusTestA). Error=Error occurred for file RNAseq_SampleFusTestA
. Error = Error GZIP header, first magic byte doesn't match for computer xxx.cbio.xxx.org@@@
StackTrace=  at Omicsoft.Util.Zip.GZip.GZipInputStream.ReadHeader () [0x00000] in <filename unknown>:0 
StackTrace=  at Omicsoft.Util.Zip.GZip.GZipInputStream.ReadHeader () [0x00000] in <filename unknown>:0 
  at Omicsoft.Util.Zip.GZip.GZipInputStream.Read (System.Byte[] buffer, Int32 offset, Int32 count) [0x00000] in <filename unknown>:0 
...

Answer 1

[Jean-Karim Heriche]

It looks like you're trying to read gzip-compressed data when the data is in fact not gzip-compressed. If there's such an option, try telling your program that the files are not compressed or compress your files with gzip first.

[noushin.farnoud]

Thanks. In fact when I gzipped the data, the error was gone. Now I have an understanding what "first magic byte error" was referring to!