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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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Error #2

Closed fengyuchengdu closed 6 years ago

fengyuchengdu commented 7 years ago

Begin addNonORFcopy at Fri Aug 4 16:00:11 2017 Traceback (most recent call last): File "isescan.py", line 57, in isPredictSingle(args4isPredictSingle) File "isescan.py", line 22, in isPredictSingle isPredict.isPredict(filelist, path2proteome, path2hmm) File "/home/zong/programs_and_scripts/ISEScan/ISEScan-master/isPredict.py", line 282, in isPredict pred.pred(args4pred) File "/home/zong/programs_and_scripts/ISEScan/ISEScan-master/pred.py", line 2604, in pred mOrfHits = addNonORFcopy(mispairs, mOrfHits) File "/home/zong/programs_and_scripts/ISEScan/ISEScan-master/pred.py", line 1956, in addNonORFcopy if len(copypairs[seqid]) == 0: KeyError: 'SWU01_chr'

The example worked fine, but when I used my own sequence (a complete bacterial chromosome) it failed as above. Could you please help me with this? Thanks much

xiezhq commented 7 years ago

Sorry to respond late. I didn't check my github site every day. Could you send me your sequence file in fasta format? Or you can put somewhere to let me download it.

Best, Zhiqun Xie

dtravisany commented 6 years ago

Hello, I had the same error. I think that could be related with blast warning "/lib64/libz.so.1: no version information available" or with different (more than one) python installation. To fix this issue, I add the path of my condas lib to LD_LIBRARY_PATH Example: export LD_LIBRARY_PATH=/path_to_anaconda/lib:$LD_LIBRARY_PATH

Cheers, Dante

xiezhq commented 6 years ago

Good points, Dante. Thanks for your comments in ISEScan.

Best, Xie