/public/home/yqming/Software/tama-master/tama_collapse.py

[wangguiqian]

(work) [yqming@mn02 01maping_data]$ conda activate python2
(python2) [yqming@mn02 01maping_data]$ python ~/Software/tama-master/tama_collapse.py -b sx-28h-ASFV_sort.bam -f ../ASFV_HLJ.fa -p ../03tama_data/sx-28h-ASFV -x no_cap
tc_version_date_2023_03_28 Sam file is missing Default collapse exon ends flag will be used: common_ends Default coverage: 99 Default identity: 85 Default identity calculation method: ident_cov Default 5 prime threshold: 10 Default exon/splice junction threshold: 10 Default 3 prime threshold: 10 Default duplicate merge flag: merge_dup Default splice junction priority: nopriority Default splice junction error threshold: 10 Default splice junction local density error threshold: 1000 Default simple error symbol for matches is the underscore "" . Using BAM format for reading in. Traceback (most recent call last): File "/public/home/yqming/Software/tama-master/tama_collapse.py", line 174, in import pysam File "/public/home/yqming/.local/lib/python2.7/site-packages/pysam/init.py", line 4, in from pysam.libchtslib import * ImportError: /public/home/yqming/.local/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8 (python2) [yqming@mn02 01maping_data]$ python Python 2.7.15 | packaged by conda-forge | (default, Mar 5 2020, 14:56:06) [GCC 7.3.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import pysam Traceback (most recent call last): File "", line 1, in File "/public/home/yqming/.local/lib/python2.7/site-packages/pysam/init.py", line 4, in from pysam.libchtslib import * ImportError: /public/home/yqming/.local/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8