Closed juadiegaitan closed 3 years ago
Sorry Ramon, an update of the error:
Command error:
Traceback (most recent call last):
File "/home/xxxx/TransPi/condaEnv/env-9a1bd41ef2ac4d341bfff3fbe3a95182/bin/transabyss", line 18, in
Hello Juan,
By the look of the error, I see you are running the pipeline using individual conda environments per process (i.e. -profile conda
). Is that correct? I have seen a couple of issues with single conda environments per process before. I will check how these can be solved.
In the meantime, I will recommend creating a single conda environment to solve this issue. This is done for you by the precheck script. Then you will run TransPi using the -profile conda --myConda
options.
Let me know if you have any further issues.
Best, Ramon
P.S. I suggest pulling the repository again since I fixed some minor bugs.
Thank you Ramon for the feedback! Just to confirm something. Do I need to change the PATH to Conda installation from precheck in the nextflow.config file? Thanks and best wishes Juan
Hello,
Each time you run the precheck script it will automatically add the PATH of the conda installation, BUSCO databases, etc. to the nextflow.config
. You then need to change, if needed, the nextflow.config
for the resources available on your system like CPUs and RAM. Anything let me know.
Best,
Ramon
Hi Ramon All solved. Thanks for the detailed guidance also in the documents. It is running well now. Best Juan
Great! Any other issues let me know. Best, Ramon
Hi Ramon Super cool pipeline! I wonder if you had any issues with the Trans-ABySS assemblies. I am getting errors for that step when running it. Basically the pipeline kills/finish the step. There is no major information in the log file, just that the single attempt and the end of the run for that step. Thoughts about this? Thanks for the feedback! Best Juan
Log
echo -e "\n-- Starting Trans-ABySS assemblies --\n"
for x in
echo 25,35,55,75,85 | tr "," " "
;do echo -e "\n-- Trans-ABySS k${x} --\n" transabyss -k ${x} --pe left-S69L.norm.fq right-S69L.norm.fq --outdir S69Ltransabyss${x} --name k${x}.transabyss.fa --threads 15 -c 12 --length 200 doneecho -e "\n-- Finished with the assemblies --\n"
for x in
echo 25,35,55,75,85 | tr "," " "
;do sed -i "s/>/>TransABySS.k${x}./g" S69Ltransabyss${x}/k${x}.transabyss.fa-final.fa donecat S69Ltransabyss/k.transabyss.fa-final.fa >S69L.TransABySS.fa
for x in
echo 25,35,55,75,85 | tr "," " "
;do cp S69Ltransabyss${x}/k${x}.transabyss.fa-final.fa S69L.TransABySS.k${x}.fa donerm -rf S69Ltransabyss* Status
Exit: 1 (FAILED) Attempts: 1 (action: FINISH)