Segmentation fault (core dumped)

[snashraf]

Hi All, I installed prebuilt binary from https://github.com/mothur/mothur/releases/download/v1.39.4/Mothur.linux_64.zip and then I launched it using ./mothur and then I used below command
mothur > make.file(inputdir=/gpfs/projects/Miseq_Data/, prefix=stability)
Setting input directory to: /gpfs/projects/Miseq_Data/
Segmentation fault (core dumped)
After running this command I am getting Segmentation fault (core dumped) error ?
Can some one please help me on this ?

[eugentoss]

The same thing.
I've tried it on 3 different computers with Ubuntu 14.04 and Centos 5.

[mothur-westcott]

I built a statically linked version of mothur for Linux. Can you give Mothur.linux_64_static.zip a try? https://github.com/mothur/mothur/releases/tag/v1.39.4

[snashraf]

Thanks ,
Still, same error persists for me.

[mothur-westcott]

Can you run it in debug mode?

mothur > set.dir(debug=t)

mothur > make.file(inputdir=/gpfs/projects/Miseq_Data/, prefix=stability)

[eugentoss]

Should we reinstall mothur again?

My debug mode gives me this:

mothur > set.dir(debug=t)
Setting [DEBUG] flag.
mothur > make.file(inputdir=MiSeq_SOP, prefix=stability)
[DEBUG]: removed MiSeq_SOP/temp1489733232
[DEBUG]: removed MiSeq_SOP/temp1489733232
Setting input directory to: MiSeq_SOP/
[DEBUG]: removed MiSeq_SOP/temp1489733232
find "MiSeq_SOP" -maxdepth 1 -name "*.fastq" > "MiSeq_SOP/fileList.temp"
[DEBUG]: removed MiSeq_SOP/fileList.temp
[DEBUG]: File 0 = MiSeq_SOP/F3D0_S188_L001_R1_001.fastq.
[DEBUG]: File 2 = MiSeq_SOP/F3D141_S207_L001_R1_001.fastq.
[DEBUG]: File 4 = MiSeq_SOP/F3D142_S208_L001_R1_001.fastq.
[DEBUG]: File 6 = MiSeq_SOP/F3D143_S209_L001_R1_001.fastq.
[DEBUG]: File 8 = MiSeq_SOP/F3D144_S210_L001_R1_001.fastq.
[DEBUG]: File 10 = MiSeq_SOP/F3D145_S211_L001_R1_001.fastq.
[DEBUG]: File 12 = MiSeq_SOP/F3D146_S212_L001_R1_001.fastq.
[DEBUG]: File 14 = MiSeq_SOP/F3D147_S213_L001_R1_001.fastq.
[DEBUG]: File 16 = MiSeq_SOP/F3D148_S214_L001_R1_001.fastq.
[DEBUG]: File 18 = MiSeq_SOP/F3D149_S215_L001_R1_001.fastq.
[DEBUG]: File 20 = MiSeq_SOP/F3D150_S216_L001_R1_001.fastq.
[DEBUG]: File 22 = MiSeq_SOP/F3D1_S189_L001_R1_001.fastq.
[DEBUG]: File 24 = MiSeq_SOP/F3D2_S190_L001_R1_001.fastq.
[DEBUG]: File 26 = MiSeq_SOP/F3D3_S191_L001_R1_001.fastq.
[DEBUG]: File 28 = MiSeq_SOP/F3D5_S193_L001_R1_001.fastq.
[DEBUG]: File 30 = MiSeq_SOP/F3D6_S194_L001_R1_001.fastq.
[DEBUG]: File 32 = MiSeq_SOP/F3D7_S195_L001_R1_001.fastq.
[DEBUG]: File 34 = MiSeq_SOP/F3D8_S196_L001_R1_001.fastq.
[DEBUG]: File 36 = MiSeq_SOP/F3D9_S197_L001_R1_001.fastq.
[DEBUG]: File 38 = MiSeq_SOP/Mock_S280_L001_R1_001.fastq.
zsh: segmentation fault ./Mothur.linux_64_static/mothur/mothur

[mothur-westcott]

I found the source of the problem and have released version 1.39.5 which corrects it. https://github.com/mothur/mothur/releases/tag/v1.39.5 Thanks for your help in catching this!