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WGLab / SeqMule

Automated human exome/genome variants detection from FASTQ files
http://seqmule.usc.edu
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file to install g++ #161

Open assafgrw opened 7 years ago

assafgrw commented 7 years ago

Hello I am a new user of seqmule, I try to run it on amazon ec2 but fail to install g++, any advises? would it run without it? i tried to run the example command line: "seqmule pipeline -a normal_R1.fastq.gz -b normal_R2.fastq.gz -prefix example -N 2 -capture default -threads 4 -e" but got the following error:

[bam_header_read] EOF marker is absent. The input is probably truncated. [E::main_mem] fail to open file `example_result/example.0.fastq.gz'. [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort!

Does it has to do with this?

thanks

kaichop commented 7 years ago

unzip the input file.

On Tue, Aug 29, 2017 at 4:24 PM, assafgrw notifications@github.com wrote:

Hello I am a new user of seqmule, I try to run it on amazon ec2 but fail to install g++, any advises? would it run without it? i tried to run the example command line: "seqmule pipeline -a normal_R1.fastq.gz -b normal_R2.fastq.gz -prefix example -N 2 -capture default -threads 4 -e" but got the following error:

[bam_header_read] EOF marker is absent. The input is probably truncated. [E::main_mem] fail to open file `example_result/example.0.fastq.gz'. [samopen] no @sq https://github.com/sq lines in the header. [sam_read1] missing header? Abort!

Does it has to do with this?

thanks

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assafgrw commented 7 years ago

To install g++?

Which input file?

kaichop commented 7 years ago

you are using fastq.gz as input file, not fastq file, yet the error message says "fail to open file `example_result/example.0.fastq.gz'." and "missing header".

On Tue, Aug 29, 2017 at 5:44 PM, assafgrw notifications@github.com wrote:

To install g++?

Which input file?

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