no hdf5 out and file not found error

[liuyuchenlab]

hi i use this scTE -i possorted_genome_bam.bam -x /disk5/lyc/index/mouse/scte/mm39.exclusive.idx --hdf5 True -CB CR -p 4 -o scte/ and it showed No such file or directory:"scte/_scTEtmp /o4/scte/.bed.gz' and there only have a scte.csv without the hdf5 Could you tell me how to fix it? Thank you.

[jphe]

Can you provide more details with the scTE output log file?

[liuyuchenlab]

scTE -i possorted_genome_bam.bam -x /disk5/lyc/index/mouse/scte/mm39.exclusive -p 4 -o /RNA_seq_1/lyc/project/lxm/scte/e14/e14 --hdf5 True -CB CR

Traceback (most recent call last): File "/home/lyc/miniconda3/bin/scTE", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTE') File "/home/lyc/miniconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 650, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/lyc/miniconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1446, in run_script exec(code, namespace, namespace) File "/home/lyc/miniconda3/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/EGG-INFO/scripts/scTE", line 173, in main() File "/home/lyc/miniconda3/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/EGG-INFO/scripts/scTE", line 155, in main len_res, genenumber, filename = Countexpression(filename=args.out, allelement=allelement, genenumber=args.genenumber, cellnumber=args.cellnumber, hdf5=args.hdf5) File "/home/lyc/miniconda3/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/scTE/base.py", line 427, in Countexpression o = gzip.open('%s_scTEtmp/o4/%s.bed.gz'%(filename, filename), 'rt') File "/home/lyc/miniconda3/lib/python3.9/gzip.py", line 58, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/home/lyc/miniconda3/lib/python3.9/gzip.py", line 173, in init fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: '/RNA_seq_1/lyc/project/lxm/scte/e14/e14_scTEtmp/o4//RNA_seq_1/lyc/project/lxm/scte/e14/e14.bed.gz'

[liuyuchenlab]

Sorry, I'm not very professional, will this help?

[EddieLv]

Perhaps u can try not using your own genome

[liuyuchenlab]

Perhaps u can try not using your own genome

It looks like he can't export to other locations?Because the output to the current directory is successful。

[EddieLv]

Sorry, I misunderstood it before. I think your question is caused by your wrong parameter setting of [-o], which should not be ended with '/', because it should be prefix of the output filename. So you should set [-o scte/] to [-o scte] :)

[MF114]

Hi, I'm encountering the same issue, have you solved yet?

[liuyuchenlab]

Hi, I'm encountering the same issue, have you solved yet?

yes,just put the output to the current directory

[MF114]

Hi, I'm encountering the same issue, have you solved yet?

yes,just put the output to the current directory

Thanks~