Closed roxyisat-rex closed 2 years ago
Hi,
I'm not familiar with the PBS job scheduler. Since the std out and std err are different files, it's a little bit hard to grasp at which step the first issues start happening.
To help diagnose this problem:
Best, Christoph
Feel free to reopen the issue if you still need assistance.
Hi Christoph
I am writing in hopes of reopening this issue. (Sorry about the delay in getting back, I was working on another project which was quite urgent). I re-ran with the test/ sample data provided in the usage link. Below is the error from terminal:
Loading anaconda3/personal
Loading requirement: fix_unwritable_tmp fix_setxattr
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Error in uik(bccount$cellindex, bccount$cs/1000) :
Method is not applicable for such a small vector. Please give at least a 5 numbers vector
Calls: cellBC -> .cellBarcode_unknown -> .FindBCcut -> uik
Execution halted
Warning message:
NAs introduced by coercion
Error in fread(paste0(opt$out_dir, "/zUMIs_output/", opt$project, "kept_barcodes.txt")) :
File '/rds/general/user/xyz16/home/bob/zUMIs_output/SS3_human_2samples_testkept_barcodes.txt' does not exist or is non-readable. getwd()=='/rds/general/user/xyz16/home/bob'
Execution halted
Loading required package: yaml
Loading required package: Matrix
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 '/rds/general/user/xyz16/home/bob/zUMIs_output/expression/SS3_human_2samples_test.dgecounts.rds', probable reason 'No such file or directory'
Execution halted
Error in data.table::fread(paste0(opt$out_dir, "/zUMIs_output/", opt$project, :
File '/rds/general/user/xyz16/home/bob/zUMIs_output/SS3_human_2samples_testkept_barcodes.txt' does not exist or is non-readable. getwd()=='/rds/general/user/xyz16/home/bob'
Execution halted
This is quite similar to the issue above (when I was using my own Smartseq 3 data) including
project.dgecounts.rds
files. The other part of the terminal output is as such:
You provided these parameters:
YAML file: runExample_fix.yaml
zUMIs directory: /rds/general/user/xyz16/home/bob/zUMIs
STAR executable STAR
samtools executable samtools
pigz executable pigz
Rscript executable Rscript
RAM limit: 20
zUMIs version 2.9.7
Thu 28 Oct 07:51:18 BST 2021
WARNING: The STAR version used for mapping is 2.7.3a and the STAR index was created using the version 2.7.1a. 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...
Thu 28 Oct 07:51:30 BST 2021
Mapping...
[1] "2021-10-28 07:51:33 BST"
Oct 28 07:51:33 ..... started STAR run
Oct 28 07:51:34 ..... loading genome
Oct 28 07:51:34 ..... processing annotations GTF
Oct 28 07:51:35 ..... inserting junctions into the genome indices
Oct 28 07:51:38 ..... started 1st pass mapping
Oct 28 07:53:39 ..... finished 1st pass mapping
Oct 28 07:53:39 ..... inserting junctions into the genome indices
Oct 28 07:53:43 ..... started mapping
Oct 28 07:55:48 ..... finished mapping
Oct 28 07:55:48 ..... finished successfully
Thu 28 Oct 07:55:48 BST 2021
Counting...
[1] "2021-10-28 07:56:16 BST"
Thu 28 Oct 07:56:16 BST 2021
[1] "loomR found"
Thu 28 Oct 07:56:19 BST 2021
Descriptive statistics...
[1] "I am loading useful packages for plotting..."
[1] "2021-10-28 07:56:19 BST"
Thu 28 Oct 07:56:30 BST 2021
Also similar to when I was using my own data. Pausing at descriptive statistics. To answer your question previous: When I was using my own ss3 data, I did not get the *.filtered.tagged.unmapped.bam file in the output directory. I got the following output files:
when using the test data describe above, I got:
The cluster is Linux. Thank you!
Feel free to reopen the issue if you still need assistance.
This is my YAML file for the test data:
project: SS3_human_2samples_test
sequence_files:
file1:
name: /rds/general/user/xyz16/home/bob/barcoderead_HEK.1mio.fq.gz
base_definition:
- BC(1-6)
- UMI(7-16)
file2:
name: /rds/general/user/xyz16/home/bob/cDNAread_HEK.1mio.fq.gz
base_definition:
- cDNA(1-50)
reference:
STAR_index: /rds/general/user/xyz16/home/bob/hg38_chr22_STAR7
GTF_file: /rds/general/user/xyz16/home/bob/GRCh38.95.chr22.gtf
additional_STAR_params: ''
additional_files: ~
out_dir: /rds/general/user/xyz16/home/bob
num_threads: 8
mem_limit: 20
filter_cutoffs:
BC_filter:
num_bases: 1
phred: 20
UMI_filter:
num_bases: 1
phred: 20
barcodes:
barcode_num: ~
barcode_file: ~
automatic: yes
BarcodeBinning: 0
nReadsperCell: 100
counting_opts:
introns: yes
downsampling: '0'
strand: 0
Ham_Dist: 0
velocyto: no
primaryHit: yes
twoPass: yes
make_stats: yes
which_Stage: Filtering
samtools_exec: samtools
zUMIs_directory: /rds/general/user/xyz16/home/bob/zUMIs
pigz_exec: pigz
STAR_exec: STAR
Rscript_exec: Rscript
read_layout: PE
Hello
I want to report an issue with zUMI. I am running on our college's HPC which is PBS and the output and error files are separate outputs so I will post both. The error log says
The output log says:
This is my YAML:
I think this is a potential problem with samtools but I am using the miniconda env that came with the package. Or maybe it is something else? I saw there was a similar issue #78 in the closed issues but that was due to a cDNA problem in the yaml and then a STAR problem but I don't think that's what's happening here. If you guys could advice, it would be great!! Thank you very much!!