weird gtz behavior
jchenpku opened this issue · 2 comments
I'm trying to compress a fastq file by gtz. However I obtained 3 totally different outcome by just modify the output
The first one was a success!
cat DMS_273.2_1.fastq | gtz -o ./G20481.DMS_273.2_1.fastq.gtz
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Compressor initializing ...
compressing ...
id: 375442529 / 3183320019
base: 819648004 / 8518710584
quality: 2158646143 / 8518710584
() source/compressed : 20468858971/3353746175. ratio : 16.385%
The cost time of compressing () is 00:06:11 (hh::mm:ss)
Compress finished, the total cost time is 00:06:11 (hh:mm:ss)
real 6m14.742s
user 134m18.192s
sys 1m8.160s
####################
This one caused an immediate error
cat DMS_273.2_1.fastq | gtz -o G20481.DMS_273.2_1.fastq.gtz
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Compressor initializing ...
gtz: line 8: 47524 Segmentation fault (core dumped)
real 0m0.198s
user 0m0.004s
sys 0m0.000s
#####################
This one was aborted
cat DMS_273.2_1.fastq | gtz -c > G20481.DMS_273.2_1.fastq.gtz
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Compressor initializing ...
compressing ...
id: 375442529 / 3183320019
base: 819648212 / 8518710584
quality: 2158646143 / 8518710584
() source/compressed : 20468858971/3353746396. ratio : 16.385%
The cost time of compressing () is 00:07:01 (hh::mm:ss)
Compress finished, the total cost time is 00:07:02 (hh:mm:ss)
terminate called without an active exception
gtz: line 8: 23992 Aborted (core dumped)
real 7m6.006s
user 136m5.360s
sys 1m6.200s
#############
This is the status by pigz:
cat DMS_273.2_1.fastq | pigz -p 4 -c > G20481.DMS_273.2_1.fastq.gz
real 6m4.838s
user 23m46.496s
sys 0m29.420s
#############
This is the final file:
3.2G Apr 4 19:55 G20481.DMS_273.2_1.fastq.gtz
5.1G Apr 4 19:36 G20481.DMS_273.2_1.fastq.gz
The compression ratio is very good.
cat DMS_273.2_1.fastq | gtz -c > G20481.DMS_273.2_1.fastq.gtz
"-c" can be only used with "-d". In gtz design, '-c' is used to write decompressed data to stdout stream. We will improve the command line parameter check function in the next release.
cat DMS_273.2_1.fastq | gtz -o G20481.DMS_273.2_1.fastq.gtz
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Compressor initializing ...
gtz: line 8: 47524 Segmentation fault (core dumped)$basepath/_gtz $ @
We have found the similar problem in gtz when deal with some quality numbers. Please try to use 0.2.2b version:
https://github.com/Genetalks/gtz/archive/0.2.2b_tech_preview.tar.gz
Feel free to tell us whether the problem has been solved.