GOTTCHA

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I was able to fix this problem on my own using the command line, but the tar.gz files have different numbers in the README than they do online. This may...

PsychNStuff

Hello, Thanks for releasing your method! I was wondering if there is a way to get the NCBI TaxIDs for the reported organisms, rather than just their names? This facilitates...

nlapier2

Can't open splitrim stats: No such file or directory

2

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...

Coaxecva

Installation failed with INSTALL.sh

1

Hi, I did git clone gottcha, then ran INSTALL.sh. I got this error whiling running INSTALL.sh. Can you help fix this? > /usr/bin/ld: ext/opt/dmd2/linux/bin64/../lib64/libphobos2.a(cpuid_a5_687.o): relocation R_X86_64_32 against symbol `_D4core5cpuid18getcacheinfoCPUID2FNbNeZv14decipherCpuid2MFhZv3idsyG63h' can...

Coaxecva

As stated in the title, can I use pair-end reads as input? I have forward and reverse reads.

yingeddi2008

Issue with BWA on prebuilt dbs

3

Hello, I'm having some issues with BWA running on one the prebuilt databases and the error message is not particularly helpful. Any idea what's going wrong? ``` $ /home/dcd3001/bin/gottcha -t...

dcdanko

Fail to extract GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.tar.gz

1

I fail to unzip and extract GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.tar.gz. Tried `tar- xvf GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.tar.gz` but I got the following error. ```database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.amb database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.ann database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.bwt database/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.pac tar: Skipping to next header tar: Archive contains ‘m|NC_008148.’...

emilhaegglund

segfault, fault detected at statistics calculation

1

I get a segmentation fault in the splitrim program. Could it be the number of reads in the file is too high ? My fastq file has 155 million reads....

raeece

Identifying Bacillus at the STRAIN level with GOTTCHA

1

Hello, I would like to know if it's possible to achieve strain-level sensitivity for Bacillus with GOTTCHA. Thanks!

estyholt

Not a HASH reference at gottcha_db.pl line 1573.

6

I'm currently stuck at the gottcha_db.pl part, building a custom database, with the following error: ... Tues 06/02/2015(15:51:17) ------------------------------------------------------------------ Tues 06/02/2015(15:51:17) Importing XML file...done. Not a HASH reference at gottcha_db.pl...

playerra