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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Can't RUN zUMIs #241

Closed Logancreator closed 3 years ago

Logancreator commented 3 years ago

Dear sir: I have a trouble about the running of zUMIs.Because when i run it, it will give me the reply as follow.

$./zUMIs-master.sh -y zUMIs.yaml

Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs

Error: Execution halted YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers.

In fact, i have check my YAML file .it doesn't have mistakes,and i use the command "cat UMIs_YAMLerror.log" ,it also doesn't have any useful information for me.

YAML file:zUMIs.yaml.txt

and my sequencing file is from smart-seq3. So can you give me some suggestions to make the software run ？I 've spent two weeks on this thing.Thanks!!!

cziegenhain commented 3 years ago

The error means that your YAML file is incorrect. you can upload the zUMIs_YAMLerror.log here so I can take a look.

From the first glance I see that you are eg. missing a space between the colon and the value of your fields (eg. project:). I would also advise against using - characters within file names.

Even though not technical errors that will produce errors, there are other things in your YAML that are not correct settings to run Smart-seq3. Please check carefully the documentation and examples: https://github.com/sdparekh/zUMIs/wiki/Usage#setup-using-the-yaml-config-file https://github.com/sandberg-lab/Smart-seq3/blob/master/allele_level_expression/mouse_cross.yaml https://www.protocols.io/view/smart-seq3-protocol-bcq4ivyw?step=18

cziegenhain commented 3 years ago

Also please always run the latest version of the pipeline.

Logancreator commented 3 years ago

Also please always run the latest version of the pipeline.

ok thanks！ Advice that will benefit me for life....

Logancreator commented 3 years ago

@cziegenhain Excuse me.sir. I have a new error on the verge of success....You see as follow:

Traceback (most recent call last): File "/md01/changjy/software/zUMIs/correct_UBtag.py", line 123, in main() File "/md01/changjy/software/zUMIs/correct_UBtag.py", line 99, in main bcs = load_bcs(args.bcs) File "/md01/changjy/software/zUMIs/correct_UBtag.py", line 16, in load_bcs with open(bcpath) as f: FileNotFoundError: [Errno 2] No such file or directory: '/md01/changjy/data/result/zUMIs_output/Smart-seq3kept_barcodes_binned.txt' [1] "4.5e+08 Reads per chunk" [E::hts_open_format] Failed to open file "/md01/changjy/data/result/Smart-seq3.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam" : No such file or directory samtools index: failed to open "/md01/changjy/data/result/Smart-seq3.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam": No such file or directory [1] "2021-01-25 17:08:07 CST" [1] "Here are the detected subsampling options:" [1] "Automatic downsampling" [1] "Working on barcode chunk 1 out of 1" [1] "Processing 184 barcodes in this chunk..." Error in value[3L] : failed to open BamFile: file(s) do not exist: ‘/md01/changjy/data/result/Smart-seq3.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam’ Calls: reads2genes_new ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted Mon Jan 25 17:08:08 CST 2021 Loading required package: yaml Loading required package: Matrix [1] "loomR found" Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/md01/changjy/data/result/zUMIs_output/expression/Smart-seq3.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 25 17:08:13 CST 2021 Descriptive statistics... [1] "I am loading useful packages for plotting..." [1] "2021-01-25 17:08:13 CST" Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/md01/changjy/data/result/zUMIs_output/expression/Smart-seq3.dgecounts.rds', probable reason 'No such file or directory' Execution halted Mon Jan 25 17:08:18 CST 2021

I run the smart-seq3 data,my yaml file is okay... This error tell me that I don't have these files.....

Look forward to your reply

cziegenhain commented 3 years ago

Hi,

Seems like there was an issue when running zUMIs with the UMI hamming correction switched on but not doing cell barcode error correction. I have pushed an update to github that should take or of that.

Please fetch the update and rerun. Best, Christoph

Logancreator commented 3 years ago

THx！I have get the result ! May I can use this software to validate my experiment result ,hope this software is getting better and better with the arising of smart-seq3 and other sequence method.Thanks!!!

cziegenhain commented 3 years ago

Good to hear it works!