注意这个帖子的有效性可能在未来某一天丧失。
简单记录下 telescope 的安装，因为 https://github.com/mlbendall/telescope 提过的官方说明直接装后测试是有问题的。
一步步安装和debug过程：
mamba create -n telescope -c bioconda -c conda-forge telescope python=3.8
conda activate telescope
mamba install numpy=1.19
mamba install -c conda-forge -c bioconda 'pysam<0.17'现在回头看可以缩减为一句命令：
mamba create -n telescope -c bioconda -c conda-forge telescope python=3.8 numpy=1.19 pysam<0.17。
测试：
(telescope) zhou2 22:12:47 ~/test
$eval $(telescope test)
2024-02-18 22:13:03 INFO
Version: 1.0.3
Input Options
samfile: /home/zhou2/miniconda3/envs/telescope/lib/python3.8/site-packages/telescope/data/alignment.bam
gtffile: /home/zhou2/miniconda3/envs/telescope/lib/python3.8/site-packages/telescope/data/annotation.gtf
attribute: locus
no_feature_key: __no_feature
ncpu: 1
tempdir: None
Reporting Options
quiet: False
debug: False
logfile: <stderr>
outdir: .
exp_tag: telescope
updated_sam: False
Run Modes
reassign_mode: exclude
conf_prob: 0.9
overlap_mode: threshold
overlap_threshold: 0.2
annotation_class: intervaltree
Model Parameters
pi_prior: 0
theta_prior: 200000
em_epsilon: 1e-07
max_iter: 100
use_likelihood: False
skip_em: False
(from run in telescope_assign.py:197)
[E::idx_find_and_load] Could not retrieve index file for '/home/zhou2/miniconda3/envs/telescope/lib/python3.8/site-packages/telescope/data/alignment.bam'
2024-02-18 22:13:03 INFO Loading annotation... (from run in telescope_assign.py:205)
2024-02-18 22:13:03 INFO Loaded annotation in 0 minutes and 0 secs (from run in telescope_assign.py:208)
2024-02-18 22:13:03 INFO Loaded 99 features. (from run in telescope_assign.py:209)
2024-02-18 22:13:03 INFO Loading alignments... (from run in telescope_assign.py:214)
[E::idx_find_and_load] Could not retrieve index file for '/home/zhou2/miniconda3/envs/telescope/lib/python3.8/site-packages/telescope/data/alignment.bam'
2024-02-18 22:13:05 INFO Loaded alignment in 0 minutes and 1 secs (from run in telescope_assign.py:217)
2024-02-18 22:13:05 INFO Alignment Summary: (from print_summary in model.py:519)
2024-02-18 22:13:05 INFO 1000 total fragments. (from print_summary in model.py:520)
2024-02-18 22:13:05 INFO 1000 mapped as pairs. (from print_summary in model.py:521)
2024-02-18 22:13:05 INFO 0 mapped as mixed. (from print_summary in model.py:522)
2024-02-18 22:13:05 INFO 0 mapped single. (from print_summary in model.py:523)
2024-02-18 22:13:05 INFO 0 failed to map. (from print_summary in model.py:524)
2024-02-18 22:13:05 INFO -- (from print_summary in model.py:525)
2024-02-18 22:13:05 INFO 1000 fragments mapped to reference; of these (from print_summary in model.py:526)
2024-02-18 22:13:05 INFO 0 had one unique alignment. (from print_summary in model.py:528)
2024-02-18 22:13:05 INFO 1000 had multiple alignments. (from print_summary in model.py:529)
2024-02-18 22:13:05 INFO -- (from print_summary in model.py:530)
2024-02-18 22:13:05 INFO 1000 fragments overlapped annotation; of these (from print_summary in model.py:531)
2024-02-18 22:13:05 INFO 0 map to one locus. (from print_summary in model.py:533)
2024-02-18 22:13:05 INFO 1000 map to multiple loci. (from print_summary in model.py:535)
2024-02-18 22:13:05 INFO
(from print_summary in model.py:537)
2024-02-18 22:13:05 INFO Running Expectation-Maximization... (from run in telescope_assign.py:250)
2024-02-18 22:13:05 INFO Iteration 1, diff=1.3795 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 2, diff=0.7388 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 3, diff=0.24275 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 4, diff=0.065133 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 5, diff=0.017653 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 6, diff=0.0050039 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 7, diff=0.0014807 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 8, diff=0.00045365 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 9, diff=0.00014275 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 10, diff=4.5844e-05 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 11, diff=1.4953e-05 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 12, diff=4.9364e-06 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 13, diff=1.645e-06 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 14, diff=5.5228e-07 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 15, diff=1.8652e-07 (from em in model.py:709)
2024-02-18 22:13:05 INFO Iteration 16, diff=6.3301e-08 (from em in model.py:709)
2024-02-18 22:13:05 INFO EM converged after 16 iterations. (from em in model.py:722)
2024-02-18 22:13:05 INFO Final log-likelihood: 95252.596293. (from em in model.py:723)
2024-02-18 22:13:05 INFO EM completed in 0 minutes and 0 secs (from run in telescope_assign.py:253)
2024-02-18 22:13:05 INFO Generating Report... (from run in telescope_assign.py:256)
2024-02-18 22:13:05 INFO telescope assign complete (0 minutes and 1 secs) (from run in telescope_assign.py:263)