error in merge_barcode_files_10x

[cheesemania]

Hi, I'm getting an error in processing 10X data

~/./sircel/sircel/sircel --10xgenomics
--barcodes R1.fastq.gz
--umis I1.fastq.gz
--reads R2.fastq.gz
--output_dir ~/10x_out --kallisto_idx kallisto_ref.idx

Inspecting and pre-processing inputs
Unzipping and merging files (temporary)
Traceback (most recent call last):
File "/home/ian/./sircel/sircel/sircel", line 9, in
load_entry_point('sircel==0.1.2', 'console_scripts', 'sircel')()
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/main.py", line 5, in main
output_files = run_all(args)
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/Sircel_master.py", line 67, in run_all
args['umis'].split(','))
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/utils/IO_utils.py", line 213, in merge_barcodefiles_10x
('\n'.join(umis), '\n'.join(cells))
NameError: name 'umis' is not defined

It looked like the ('\n'.join(umis), '\n'.join(cells)) part had undefined elements, I recompiled changing 'umis' to 'umi' and 'cells' to 'bc', and got a new error

Inspecting and pre-processing inputs
Unzipping and merging files (temporary)
Traceback (most recent call last):
File "/home/ian/./sircel/sircel/sircel", line 9, in
load_entry_point('sircel==0.1.2', 'console_scripts', 'sircel')()
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/main.py", line 5, in main
output_files = run_all(args)
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/Sircel_master.py", line 67, in run_all
args['umis'].split(','))
File "/usr/local/lib/python3.5/dist-packages/sircel-0.1.2-py3.5.egg/sircel/utils/IO_utils.py", line 213, in merge_barcodefiles_10x
('\n'.join(umi), '\n'.join(bc))
AssertionError: Reads are not in order
m
i
h
c
5
h
m
_

Though admittedly this second one may be due to me mangling your code

Any suggestions on what may be going wrong?

Thanks,

Ian

[modash]

Hi,

I am also facing the same issue. I have noticed few patch works have been done previously on this, but still getting this error. Any idea?

--
Ashick

[kuikuisven]

Hi , I also get the same error..