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root@f71f06b4874d:/home# ./PEMA_v1.bds do you recognise the problem? Haris Zafeiropoulos @hariszaf Hi @Matthias! Do you have your raw data in a folder called yes, the folder is on the Desktop Haris Zafeiropoulos @hariszaf So you have something like this and there you have your parameters file and a folder called Desktop/analysis_directory/mydata/ the parameters file is under analysis_directory, and the fastq file is under mydata Haris Zafeiropoulos @hariszaf and you run I am asking because you need to mount the whole analysis_directory not just your data. i hadnavigates to the desktop therefore i only had "/anlaysis_directory" as path. Now i copied your command and get this: "docker run" requires at least 1 argument. Usage: docker run [OPTIONS] IMAGE [COMMAND] [ARG...] Run a command in a new container Haris Zafeiropoulos @hariszaf
if you run this what do you get? Haris Zafeiropoulos @hariszaf ok. could you run root@3069a1f860d3:/home# ls -la /mnt Haris Zafeiropoulos @hariszaf :thumbsup: total
4 Haris Zafeiropoulos @hariszaf this is from the second command??? Haris Zafeiropoulos @hariszaf ok please run exit. C:\Users\xobsma\Desktop>pwd 18 replies Hi Haris, I am back. I found the problem with the Mac installation. You have to add a "~" before the path to the analysis directory in the github tutorial ...and i got another error when executing PEMA_v1.bds:
29 replies Haris Zafeiropoulos @hariszaf Hi @/all ! FYI I am about to integrate the convertIllumunaRawDataToEnaFormat.sh script in the main PEMA code. It seems like an unessecary burden! If you have any other suggestions in terms of improvement of PEMA there are more than welcome! @hariszaf . I got this error and i feel that this has something to do with the parameter.tsv file all the first steps are done!
clustering is about to start! ProgramCounter.pop(100): Node ID does not match! i have checked the clusteringAlgoForCOI_ITS and set it into algo_CROP, but the error still persist. Also I am not really sure if I have to comment (#) the 'clusteringAkgofor_16S_18SrRNa part as I am using only COI for the moment . Thanks @hariszaf . So sorry for the trouble... Haris Zafeiropoulos @hariszaf Hi @ajiwahyu ! Thank you for the feedback! You should not comment out any of the parameters! PEMA needs to know that
it has access to all of them even if you do not use them. So, you could check that all the parameters are on and make sure that your parameters file is tab separated. I would suggest to go It is essential to have a tab seperated file.. This is a quite common error but for the time being we cannot avoid this format.. :/ Thanks @hariszaf. I just tried your suggestion and the pipeline seemed working with SWARM but spit the following error when I used CROP. Also a question with Database, for COI what database are you using?. Is there any setting that I need to change if I want to use different data base?.Also for setting a targetlength at the trimmomatic part, how should one decide it?. IAm using COI, with COI primer dgHCO2198, expecting a final merge reads at 300-330 bp. This is the error i got when using CROP COI; cropPath is: /mnt/analysis/16S_final_test/7.gene_dependent/gene_COI/CROP sed: can't read
/mnt/analysis/16S_final_test/7.gene_dependent/gene_COI/CROP/abundances/x: No such file or directory Haris Zafeiropoulos @hariszaf Hi @ajiwahyu! Thanks a lot for this! There was a bug on the script that calculates the CROP parameters. I am about to rebuild an image fixing that. Regarding the COI marker gene, PEMA uses the MIDORI database, which you may find here. For the time being you cannot use an in-house reference database, however that is going to be included in the next version of PEMA. Haris Zafeiropoulos @hariszaf When it comes to the Trimmomatic parameters, you should always check on its manual Thanks @hariszaf !, ill be waiting the update from the bug! 10 replies Haris Zafeiropoulos @hariszaf :plus1: After running PEMA with vsearch, the pipeline stopped because my metadata file was named as metadata1.csv. I renamed it as metadata.csv and restarted the pipeline at phyloseq.chp. It resulted in an empty OTU table and so phyloseq did not run. As we discussed, I believe I should have restarted at tableStep.chp? Haris Zafeiropoulos @hariszaf Hi @migdesmarais! it is most likely that this is what went bad. If you run the Haris Zafeiropoulos @hariszaf Hi @ajiwahyu , hi @all. @ajiwahyu many thanks for the feedback once again. thanks @hariszaf !. Am i correct to assume that i need to do another "singularity pull" again so my PEMA container is up to date? M Danie Al Malik @daniealmalik354 Hello @hariszaf, I have trouble to run my data on Windows OS from Docker. When I run the data the result like this: Fatal error: ./pema_latest.bds, line 80, pos 27. Map 'paramsFirstAssignment' does not have key 'outputFolderName'. Please help me if you have a suggestion. Thank you Haris Zafeiropoulos @hariszaf
Yes you are absolutely right.
You now need to run Haris Zafeiropoulos @hariszaf
Hi @daniealmalik354 ! Download the 3 replies Haris Zafeiropoulos @hariszaf Hi @/all ! |