snap-pre step error

[znavidi]

Hi,

I face an error in running snap pre step with this command:

snaptools snap-pre --input-file=GSE74310ـGSE74310ـGSE99172.nsorted.bam --output-snap=GSE74310ـGSE74310ـGSE99172.snap --genome-name=hg38 --genome-size=../../ref/hg38/hg38.chrom.sizes --min-mapq=30 --min-flen=0 --max-flen=1000 --keep-chrm=TRUE --keep-single=FALSE --keep-secondary=FALSE --overwrite=True --min-cov=100 --verbose=True

and the error is:

Traceback (most recent call last): File "/home/znavidi/.local/bin/snaptools", line 38, in parse_args()
File "/home/znavidi/.local/lib/python3.7/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/home/znavidi/.local/lib/python3.7/site-packages/snaptools/snap_pre.py", line 240, in snap_pre f.createdataset("HD/CL", data=np.string(header["CL"])); UnicodeEncodeError: 'ascii' codec can't encode character '\u0640' in position 65: ordinal not in range(128)

I would appreciate any hint about what could be the problem.

Best, Zeinab

[r3fang]

Did you have this error before? Maybe try python 2.7 or python 3.6

-- Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Aug 6, 2019, at 11:18 PM, znavidi notifications@github.com wrote:

Hi,

I face an error in running snap pre step with this command:

snaptools snap-pre --input-file=GSE74310ـGSE74310ـGSE99172.nsorted.bam --output-snap=GSE74310ـGSE74310ـGSE99172.snap --genome-name=hg38 --genome-size=../../ref/hg38/hg38.chrom.sizes --min-mapq=30 --min-flen=0 --max-flen=1000 --keep-chrm=TRUE --keep-single=FALSE --keep-secondary=FALSE --overwrite=True --min-cov=100 --verbose=True

and the error is:

Traceback (most recent call last): File "/home/znavidi/.local/bin/snaptools", line 38, in parse_args() File "/home/znavidi/.local/lib/python3.7/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/home/znavidi/.local/lib/python3.7/site-packages/snaptools/snap_pre.py", line 240, in snap_pre f.createdataset("HD/CL", data=np.string(header["CL"])); UnicodeEncodeError: 'ascii' codec can't encode character '\u0640' in position 65: ordinal not in range(128)

I would appreciate any hint about what could be the problem.

Best, Zeinab

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[znavidi]

No I have not had this error before and I run it multiple times with the same setting in python 3.7.

I tried running with python 2.7 and 3.6 and it gets these error:

• for 2.7 (after running for a while it got this error):

Traceback (most recent call last): File "/home/znavidi/zeinab-2.7/bin/snaptools", line 38, in parse_args()
File "/home/znavidi/zeinab-2.7/lib/python2.7/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/home/znavidi/zeinab-2.7/lib/python2.7/site-packages/snaptools/snap_pre.py", line 215, in snap_pre header["CL"] = "\t".join(map(str, sys.argv)); File "/home/znavidi/zeinab-2.7/lib/python2.7/site-packages/future/types/newstr.py", line 102, in new return super(newstr, cls).new(cls, value) UnicodeDecodeError: 'ascii' codec can't decode byte 0xd9 in position 21: ordinal not in range(128) (zeinab-2.7) [znavidi@cedar1 labeled]$ deactivate

• for 3.6 (it quickly got this error):

Traceback (most recent call last): File "/home/znavidi/zeinab-3.6.3/bin/snaptools", line 38, in parse_args()
File "/home/znavidi/zeinab-3.6.3/lib/python3.6/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/home/znavidi/zeinab-3.6.3/lib/python3.6/site-packages/snaptools/snap_pre.py", line 240, in snap_pre f.createdataset("HD/CL", data=np.string(header["CL"])); UnicodeEncodeError: 'ascii' codec can't encode character '\u0640' in position 71: ordinal not in range(128)

Would appreciate any help.

Thanks

[znavidi]

could it be because of the size of bam file? it is 97G and all other previous run was less than this. if yes, what is the solution?

Best, Zeinab

[cynzajac]

I am encountering the same problem

Traceback (most recent call last): File "/home/herrerab/anaconda3/bin/snaptools", line 38, in parse_args() File "/home/herrerab/anaconda3/lib/python3.7/site-packages/snaptools/parser.py", line 144, in parse_args verbose=args.verbose) File "/home/herrerab/anaconda3/lib/python3.7/site-packages/snaptools/snap_pre.py", line 283, in snap_pre frag = snaptools.snap.readPairToFragment(read1, read2, is_secondary); File "/home/herrerab/anaconda3/lib/python3.7/site-packages/snaptools/snap.py", line 530, in readPairToFragment return fragment(read1.qname, chrom1, start, abs(start - end), mapq, False, is_secondary, read1.is_proper_pair); File "/home/herrerab/anaconda3/lib/python3.7/site-packages/snaptools/snap.py", line 624, in init self.chrom = chrom.encode('utf-8') AttributeError: 'NoneType' object has no attribute 'encode'

I haven't used older versions of python since I have tested the most recent python version with snaptools for different set of files. I am not sure if the bam size file matters honestly.