The filtering has been running for 3 days now, no warning is given but something must be broken

[Kdoganyi]

Hi there, I am trying to analyze my miseq data (smartseq3 method was used).

After opening a virtual env, I started a screen and ran the command below:

**zUMIs/zUMIs.sh -y /public/groups/hausslerlab/people/kivilcim/iMGL/yamls/KDiMGL1st_sp.yaml Warning messages: 1: In if (!file.exists(x$name)) { : the condition has length > 1 and only the first element will be used 2: In if (!file.exists(x$name)) { : the condition has length > 1 and only the first element will be used 3: In if (!file.exists(x$name)) { : the condition has length > 1 and only the first element will be used 4: In if (!file.exists(x$name)) { : the condition has length > 1 and only the first element will be used

You provided these parameters: YAML file: /public/groups/hausslerlab/people/kivilcim/iMGL/yamls/KDiMGL1st_sp.yaml zUMIs directory: /public/groups/hausslerlab/people/kivilcim/iMGL/zUMIs STAR executable /public/groups/hausslerlab/people/sseiler/Programs/STAR/STAR-2.7.4a/bin/Linux_x86_64_static/STAR samtools executable samtools pigz executable pigz Rscript executable Rscript RAM limit: null zUMIs version 2.9.7

Mon Mar 3 15:14:54 PST 2022 Filtering... stat: missing operand**

Even though I detached the screen, whenever I went back to the screen program appeared to be running.

My understanding is that generating one big yaml file for everything is supposed to work the best. I am attaching my yaml file: KDiMGL1st_sp.yaml.txt

I have tried doing this so many ways, and whenever I think I fixed something I run into a different problem. However, this time I actually have no idea what is going on. Why am I not getting any warning but it feels like something is broken? Am I in an infinite loop somehow?

Thank you so much already!

[cziegenhain]

Hi,

You can only give one filepath under the 'name' field. Seems like your data is already demultiplexed, you can use the non-demultiplexed data (if you dont have it you could concatenate the fastq files from many cells).

With the typical output of a MiSeq run, I would think the Filtering step should only take a few minutes! Best, Christoph

[Kdoganyi]

Thanks a lot for your response! I think that worked!

[Kdoganyi]

Hi there! I have a new issue that I just started getting yesterday. Should I end this one and start a new repository? Basically, after getting some analysis done, and getting some data out, I stopped making any process. The issue is that now when I run the program (zUMIs/zUMIs.sh -y location) the program keeps halting at the first stage, saying there was a parse error and from there on I am getting empty files. Below I pasted what I get as a warning " [W::sam_read1] Parse error at line 3 [main_samview] truncated file. [W::sam_read1] Parse error at line 3 [main_samview] truncated file. [W::sam_read1] Parse error at line 3 [main_samview] truncated file. [W::sam_read1] Parse error at line 3 [main_samview] truncated file. cat: /public/groups/hausslerlab/people/kivilcim/iMGL/outputall/zUMIs_output/.tmpMerge//KDiMGLall.*.BCstats.txt: No such file or directory Mon Mar 14 20:24:07 PDT 2022 Error in eval(bysub, parent.frame(), parent.frame()) : object 'XC' not found Calls: cellBC -> [ -> [.data.table -> eval -> eval In addition: Warning message: In data.table::fread(bccount_file, header = FALSE, col.names = c("XC", : File '/public/groups/hausslerlab/people/kivilcim/iMGL/outputall/KDiMGLall.BCstats.txt' has size 0. Returning a NULL data.table. Execution halted " This did not happen when I was using the same data 2 days ago, and my yaml file appears to be formatted correctly. I have seen some comments about this issue in the zUMIs repository. Let me know, if you believe it is a better idea to post here, at zUMIs repository, or if I should start a new issue. Depending on your answer I can include all my files, links to what I have tried and explain the situation better. Truly appreciative of your help! Thank you so much!