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LANL-Bioinformatics / GOTTCHA

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Please visit our homepage:
http://lanl-bioinformatics.github.io/GOTTCHA
GNU General Public License v3.0
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Can't open splitrim stats: No such file or directory #14

Open Coaxecva opened 4 years ago

Coaxecva commented 4 years ago

Hi,

I got this error when I ran with the option "--input file_1.fastq,file_2.fastq" :

[00:00:00] Starting GOTTCHA v1.0c [00:00:00] Auto set database level to SPECIES. [00:00:00] Number of threads: 8 [00:00:01] Checking running environment... [00:00:01] Done. All required scripts and tools found. [00:00:01] Split-trimming with parameters fixL=30, minQ=20, ascii=33. [00:00:01] Split-trimming: /file_1.fastq... [00:02:56] Done splitrimming /file_1.fastq. [00:02:56] Split-trimming: ~/file_2.fastq... [00:02:56] Done splitrimming ~/file_2.fastq. Can't open splitrim stats: No such file or directory

It is running fine with one fastq file. Can you help to solve this?

Thanks, Coax

poeli commented 4 years ago

Hi Coax,

The split-trim step finished immediately. I suspect there is something wrong with "file_2.fastq" (could be empty). Please double check.

Thanks, Paul

Coaxecva commented 4 years ago

Thanks, Paul.

I think the software doesn't get this linux command "~/" . I used "--input ~/<path-to-my-folder>/file_1.fastq,~/<path-to-my-folder>/file_2.fastq". It can only recognize the first "~/".

Coax