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_barcodefiles10x ('\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..