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Old 10-21-2012, 12:10 AM   #1
yaximik
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Registered: Nov 2010
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decompression error - help!


Hello,

I got a foo.fastq.gz file as output from a sequencer (Windows 7 machine). It is 1.9 GB. After transfer to RHEL55 box I tried gunzip, which about a halfway through exited with error with all available options deleting the temporary file about 5.4 GB:

Code:
[yaximik@G5NNJN1 MiSeq]$ gunzip -t SC2T252P15_S1_L001_R1_001.fastq.gz
gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--crc error

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--length error
[yaximik@G5NNJN1 MiSeq]$ gunzip -q SC2T252P15_S1_L001_R1_001.fastq.gz

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--crc error

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--length error
[yaximik@G5NNJN1 MiSeq]$ gunzip -dq SC2T252P15_S1_L001_R1_001.fastq.gz

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--crc error

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--length error
Using GUI (Archive Manager) I saw that both errors are caused by one particular line entry, which is not hsown in the stdout. Finally, I was able to salvage everything until this line entry using

Code:
[yaximik@G5NNJN1 MiSeq]$ gunzip -c SC2T252P15_S1_L001_R1_001.fastq.gz > ./SC2T252P15_S1_L001_R1_001.fastq

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--crc error

gunzip: SC2T252P15_S1_L001_R1_001.fastq.gz: invalid compressed data--length error
which still exited with error, but I got the 5.2 GB foo.fastq text file

Here is the file content output:

Code:
[yaximik@G5NNJN1 MiSeq]$ gunzip -cl SC2T252P15_S1_L001_R1_001.fastq.gz >./content.txt
[yaximik@G5NNJN1 MiSeq]$ cat content.txt
         compressed        uncompressed  ratio uncompressed_name
         2086259746          1331149161 -56.7% SC2T252P15_S1_L001_R1_001.fastq
[yaximik@G5NNJN1 MiSeq]$
Is anything wrong with the content?

But the main question I am asking for help with - is there an utility that will allow to edit the original foo.fastq.gz file and remove the offending line and re-extract healthy data, which are too valuable?
 
Old 10-21-2012, 12:58 AM   #2
malekmustaq
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Try using force:

Code:
gunzip -f SC2T252P15_S1_L001_R1_001.fastq.gz
If you want to extract to and fro files from an archive use "cpio".

Hope that helps.

Goodluck.
 
  


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