fastQValidator

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Killed on large fastq files

2

I'm able to run fastQValidator on fastq files up to at least 250,000,000 sequences, but when I run my entire file with about 460,000,000 sequences, the program ends and says...

rhart604

compiling problem

1

I got the following error message when compiling: g++ -O4 -pipe -Wall -I../../libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o ../bin/fastQValidator ../obj/FastQValidator.o ../../libStatGen/libStatGen.a -lm -lz ../obj/FastQValidator.o: In function `main': FastQValidator.cpp:(.text.startup+0xabc): undefined reference...

tickteng

Problem compiling in Ubuntu

2

Hi. I downloaded the version containing both the FastQValidator and LibStatGen from: https://genome.sph.umich.edu/w/images/2/20/FastQValidatorLibStatGen.0.1.1a.tgz Then I unzipped the package. Then cd into the directory and then typed "make all". Below is...

sharpo1

cannot make

1

make clean Makefile.inc:29: ../libStatGen/Makefiles/Makefile.tool: No such file or directory Unable to locate: ./../libStatGen/Makefiles/Makefile.tool To change the location, set LIB_PATH_GENERAL or LIB_PATH_FASTQ_VALIDATOR to the appropriate path to libStatGen. Or specify "make...

juancresc

Fixed a spelling mistake.

scchess

Returning symbol(s) not found for architecture x86_64 ERROR

2

When I try and install this locally on my mac it throws this error snippet ``` ... ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with...

Linesmerrill

Hi I am running ffastQValidator for a huge dataset. I prefer to have the result of all the FastQs ( returning values) in one '.out' command. But the script exits...

karthigayini

Returning: 6 : FASTQ_NO_SEQUENCE_ERROR is non-obvious

2

When validating one of my files, I get this error: [ec2-user@master scratch]$ $FASTQVALIDATOR --disableSeqIDCheck --file sample_2.clipped.fastq Finished processing M2GEN-BMS-0715-11192013-LU-FT_L6.D706_2.clipped.fastq with 230767016 lines containing 57691754 sequences. There were a total of...

golharam

Feature Request: Report the Space type

4

As getSpaceType() is an option in libStatGen it would be nice to be able to use fastQValidator to both validate the fastq and report the space (color or base), for...

tomck

Would be nice is the quality score encoding scheme is reported, Phred+33, Phred+64, etc.

golharam