Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
I manage to use the anacapa data_container and the test_data works great! I am now trying to use my own dataset, so I started with a couple of files to see everything runs smoothly. I am also using the 12S_mitofish primers, so there is no change there. I have checked my data and with my service provider and my data has already trimmed the nextera adapters and all reads start with my primer sequence. Then, I run the code and this is the output:
Thu Feb 24 18:36:29 -05 2022
Preprocessing: 1) Generate an md5sum file
Thu Feb 24 18:36:30 -05 2022
Preprocessing: 2) Change file suffixes
Thu Feb 24 18:36:30 -05 2022
QC: 1) Run cutadapt to remove 5'sequncing adapters and 3'primers + sequencing adapters, sort for length, and quality.
Generating Primer and Primer + Adapter files for cutadapt steps. Your adapter type is nextera.
At-F-06 ...
forward...
check
reverse...
check
Thu Feb 24 18:38:25 -05 2022
12S
Checking that Paired reads are still paired:
...
3' primer sequences 12S
Process metabarcode reads for with dada2
If a dada2 job fails you can find the run script in /home/dna_server/Documentos/anacapa_datacontainer/anacapa/Fish/12S_qc_dada2_output//Run_info/run_scripts and the dada2 output in /home/dna_server/Documentos/anacapa_datacontainer/anacapa/Fish/12S_qc_dada2_output//Run_info/dada2_out/
good luck!
real 1m56,296s
user 1m53,513s
sys 0m1,742s
It seems something is not working as it never starts the reads in dada2. It has to be an issue with the cutadapted reads, but I have no idea what I could be doing wrong. I am attaching the cutadapt report if that may help. Thanks for the help.
Hello again,
I manage to use the anacapa data_container and the test_data works great! I am now trying to use my own dataset, so I started with a couple of files to see everything runs smoothly. I am also using the 12S_mitofish primers, so there is no change there. I have checked my data and with my service provider and my data has already trimmed the nextera adapters and all reads start with my primer sequence. Then, I run the code and this is the output:
It seems something is not working as it never starts the reads in dada2. It has to be an issue with the cutadapted reads, but I have no idea what I could be doing wrong. I am attaching the cutadapt report if that may help. Thanks for the help.
cutadapt-report.txt