Syntax error loading yaml file

[xuwanxing]

I used sample HEK293T in Smart-seq3 pipeline to run zUMIs and got an error: Error: Syntax error loading yaml file Execution halted YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers. Here is my yaml file: https://github.com/xuwanxing/Scripts/blob/main/HEK.yaml I noticed some solutions (as below), but they didn't work for me.
https://github.com/sdparekh/zUMIs/issues/241 https://github.com/sdparekh/zUMIs/issues/232 https://github.com/sandberg-lab/Smart-seq3/issues/2 Can anybody help me? Thanks.

[cziegenhain]

Hi,

Your yaml file is missing a space in the first line after the colon - this breaks the yaml spec.

If that doesnt fix the issue, upload the zUMIs_YAMLerror.log so I can take a look what the issue seems to be.

Best, C

[xuwanxing]

Hi,

Your yaml file is missing a space in the first line after the colon - this breaks the yaml spec.

If that doesnt fix the issue, upload the zUMIs_YAMLerror.log so I can take a look what the issue seems to be.

Best, C

Thanks. I modified the yaml file but didn't fix the issue. Here is the error.log: $file1 NULL $file2 NULL $file3 NULL [1] "" [1] "" [1] "" [1] "" "" "" [1] "" [1] "" [1] "" [1] "" "" "" [1] "NULL" "NULL" "NULL" $file1 NULL $file2 NULL $file3 NULL $file1 NULL $file2 NULL $file3 NULL [1] "STAR index does not exists" [1] 1

I think maybe there are some unknown format errors in yaml file. So I turn to use online tool (http://shiny.bio.lmu.de:3838/zUMIs-config/) to generate yaml file (https://github.com/xuwanxing/Scripts/blob/main/HEK_online.yaml). It has been executed successfully! Here is the command: /nfs02data1/home/xuwanxing/smartseq3/zUMIs/zUMIs.sh -c -y HEK_online.yaml

During the process of testing, I noticed a small error: The Method section of the paper gives the STAR parameters: --limitSjdbInsertNsj 2000000 --outFilterIntronMotifs --RemoveNoncanonicalUnannotated --clip3pAdapterSeq CTGTCTCTTATACACATCT. I think the "--" before "RemoveNoncanonicalUnannotated" should be removed.

Thanks for developing such good pipeline!

[cziegenhain]

This reads like the STAR index is not found at the location you are giving! Double check if this path is correct and you have permissions.

And yes, the -- is wrong as you mention!

[xuwanxing]

This reads like the STAR index is not found at the location you are giving! Double check if this path is correct and you have permissions.

And yes, the -- is wrong as you mention!

I found I didn't have the access to the parent directory of the location of STAR index. I modified the permission and reran the pipeline. It got an error in mapping step: ... Fri Nov 12 16:12:06 CST 2021 WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the version 2.7.4a. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR 2.7.3a. Filtering... Fri Nov 12 16:56:31 CST 2021 [1] "18397953 reads were assigned to barcodes that do not correspond to intact cells." [1] "Found 5512 daughter barcodes that can be binned into 117 parent barcodes." [1] "Binned barcodes correspond to 5549049 reads."

Mapping... [1] "2021-11-12 17:03:01 CST" Nov 12 17:03:44 ..... started STAR run Nov 12 17:04:37 ..... loading genome Nov 12 17:03:44 ..... started STAR run Nov 12 17:04:37 ..... loading genome

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt" SOLUTION: use correct parameter name (check the manual)

Nov 12 17:04:39 ...... FATAL ERROR, exiting ... I thought maybe my STAR index was incompatible with this pipeline. So I rebuilt index with STAR of zUMIs package and reran the pipeline. It completed with no errors.

[cziegenhain]

Great to hear that it ran without errors now, I'm closing this issue.