Open alexlenail opened 1 year ago
I filtered the bam files using this awk command:
samtools view possorted_genome_bam.bam -h | awk '/^@/ || /CB:/ && /UB:/' | samtools view -h -b > possorted_genome_bam.filtered.bam
then I do:
scTE -i possorted_genome_bam.filtered.bam -o out -x /home/lenail/scTE/hg38.exclusive.idx --hdf5 True -CB CB -UMI UB --thread 4
but I get this error:
DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 INFO : Parameter list: Sample = /net/bmc-lab5/data/kellis/users/lenail/PFC_aging/scTE/D19-4296/out Reference annotation index = /home/lenail/scTE/hg38.exclusive.idx Minimum number of genes required = 200 Minimum number of counts required = None Number of threads = 4 INFO : Loading the genome annotation index... 2022-08-25 21:40:48 INFO : Loaded '/home/lenail/scTE/hg38.exclusive.idx' binary file with 4778929 items INFO : Finished loading the genome annotation index... 2022-08-25 21:41:42 INFO : Processing BAM/SAM files ...2022-08-25 21:41:42 INFO : Input SAM/BAM file appears to be valid INFO : Done BAM/SAM files processing ...2022-08-25 23:58:40 INFO : Splitting ...2022-08-25 23:58:40 INFO : Executing multiple thread path with 4 threads ['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '3', '4', '5', '6', '7', '8', '9', 'M', 'X', 'Y'] CB UB good gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated gzip: out_scTEtmp/o1/out.bed.gz: invalid compressed data--format violated multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/lenail/.conda/envs/py39/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/lenail/.conda/envs/py39/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(*args)) File "/home/lenail/.conda/envs/py39/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/scTE/base.py", line 366, in splitChr CRs[t[3]] += 1 IndexError: list index out of range """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/lenail/.conda/envs/py39/bin/scTE", line 4, in <module> __import__('pkg_resources').run_script('scTE==1.0', 'scTE') File "/home/lenail/.conda/envs/py39/lib/python3.9/site-packages/pkg_resources/__init__.py", line 672, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/lenail/.conda/envs/py39/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1472, in run_script exec(code, namespace, namespace) File "/home/lenail/.conda/envs/py39/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/EGG-INFO/scripts/scTE", line 169, in <module> main() File "/home/lenail/.conda/envs/py39/lib/python3.9/site-packages/scTE-1.0-py3.9.egg/EGG-INFO/scripts/scTE", line 134, in main pool.map(partial_work, chr_list) File "/home/lenail/.conda/envs/py39/lib/python3.9/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/lenail/.conda/envs/py39/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value IndexError: list index out of range
Any ideas?
I filtered the bam files using this awk command:
then I do:
but I get this error:
Any ideas?