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mlbendall / telescope

Quantification of transposable element expression using RNA-seq
MIT License
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Telescope - TypeError: 'int' object is not iterable #3

Closed GislaineCurty closed 5 years ago

GislaineCurty commented 5 years ago

Hello,

I have get error message during telescope running. Could you please help me?

source /tools/Anaconda2/ENV_for_Anaconda2 conda activate teletest telescope assign --updated_sam /home/gcurty/herv2018/doc/MCF7_teste_RNAseq/bowtie2_MCF7.sam /home/gcurty/herv2018/doc/MCF7_teste_RNAseq/transcripts.gtf conda deactivate

Qui Dez 13 13:05:28 -02 2018 2018-12-13 13:05:29 INFO Version: 1.0 Input Options samfile: /home/gcurty/herv2018/doc/MCF7_teste_RNAseq/bowtie2_MCF7.sam gtffile: /home/gcurty/herv2018/doc/MCF7_teste_RNAseq/transcripts.gtf attribute: locus no_feature_key: __no_feature ncpu: 1 tempdir: None Reporting Options quiet: False debug: False logfile: outdir: . exp_tag: telescope updated_sam: True 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: 0 em_epsilon: 1e-07 max_iter: 100 use_likelihood: False skip_em: False (from run in telescope_assign.py:193) 2018-12-13 13:05:29 INFO Loading annotation... (from run in telescope_assign.py:201) 2018-12-13 13:05:39 INFO Loaded annotation in 0 minutes and 9 secs (from run in telescope_assign.py:204) 2018-12-13 13:05:39 INFO Loaded 14896 features. (from run in telescope_assign.py:205) 2018-12-13 13:05:39 INFO Loading alignments... (from run in telescope_assign.py:210) Traceback (most recent call last): File "/home/gcurty/.conda/envs/teletest/bin/telescope", line 11, in sys.exit(main()) File "/home/gcurty/.conda/envs/teletest/lib/python3.6/site-packages/telescope/main.py", line 58, in main args.func(args) File "/home/gcurty/.conda/envs/teletest/lib/python3.6/site-packages/telescope/telescope_assign.py", line 212, in run ts.load_alignment(annot) File "/home/gcurty/.conda/envs/teletest/lib/python3.6/site-packages/telescope/utils/model.py", line 161, in load_alignment maps, scorerange, alninfo = self._load_sequential(annotation) File "/home/gcurty/.conda/envs/teletest/lib/python3.6/site-packages/telescope/utils/model.py", line 250, in _load_sequential _minAS = min(_minAS, *_scores) TypeError: 'int' object is not iterable

Thank you so much! Gislaine Curty.

mlbendall commented 5 years ago

If you can find a way to send me the BAM file and annotation you are using that would be helpful.

mlbendall commented 5 years ago

Error was due to some mispaired reads in the input BAM.