Closed hchintalapudi closed 4 years ago
telescope assign BAM_STAR/ICGC-ABMB-20100303-10-TR.bam gencode.v31.annotation.gtf --attribute gene_id --exp_tag ICGC-ABMB-20100303-10-TR --outdir Telescope/ 2020-02-04 09:32:37 INFO Version: 1.0.3 Input Options samfile: BAM_STAR/ICGC-ABMB-20100303-10-TR.bam gtffile: gencode.v31.annotation.gtf attribute: gene_id no_feature_key: no_feature ncpu: 1 tempdir: None Reporting Options quiet: False debug: False logfile: outdir: Telescope/ exp_tag: ICGC-ABMB-20100303-10-TR 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) 2020-02-04 09:32:37 INFO Loading annotation... (from run in telescope_assign.py:205) 2020-02-04 09:37:01 INFO Loaded annotation in 4 minutes and 23 secs (from run in telescope_assign.py:208) 2020-02-04 09:37:01 INFO Loaded 60603 features. (from run in telescope_assign.py:209) 2020-02-04 09:37:01 INFO Loading alignments... (from run in telescope_assign.py:214) 2020-02-04 09:39:30 INFO ...processed 2.5M fragments (from _print_progress in model.py:69) 2020-02-04 09:42:03 INFO ...processed 5.0M fragments (from _print_progress in model.py:69) 2020-02-04 09:44:34 INFO ...processed 7.5M fragments (from _print_progress in model.py:69) . . . . . 2020-02-04 12:48:07 INFO ...processed 185.0M fragments (from _print_progress in model.py:69) Traceback (most recent call last): File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/bin/telescope", line 11, in load_entry_point('telescope-ngs==1.0.3', 'console_scripts', 'telescope')() File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/main__.py", line 95, in main args.func(args) File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/telescope_assign.py", line 216, in run ts.load_alignment(annot) File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/utils/model.py", line 164, in load_alignment self._mapping_to_matrix(maps, scorerange, alninfo) File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/utils/model.py", line 339, in _mapping_to_matrix rownames = np.array(sorted(_ridx, key=_ridx.get)) MemoryError
I have sufficient RAM. Can you help me with error please? Thank you.
telescope assign BAM_STAR/ICGC-ABMB-20100303-10-TR.bam gencode.v31.annotation.gtf --attribute gene_id --exp_tag ICGC-ABMB-20100303-10-TR --outdir Telescope/
outdir: Telescope/
exp_tag: ICGC-ABMB-20100303-10-TR
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)
2020-02-04 09:32:37 INFO Loading annotation... (from run in telescope_assign.py:205)
2020-02-04 09:37:01 INFO Loaded annotation in 4 minutes and 23 secs (from run in telescope_assign.py:208)
2020-02-04 09:37:01 INFO Loaded 60603 features. (from run in telescope_assign.py:209)
2020-02-04 09:37:01 INFO Loading alignments... (from run in telescope_assign.py:214)
2020-02-04 09:39:30 INFO ...processed 2.5M fragments (from _print_progress in model.py:69)
2020-02-04 09:42:03 INFO ...processed 5.0M fragments (from _print_progress in model.py:69)
2020-02-04 09:44:34 INFO ...processed 7.5M fragments (from _print_progress in model.py:69)
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2020-02-04 12:48:07 INFO ...processed 185.0M fragments (from _print_progress in model.py:69)
Traceback (most recent call last):
File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/bin/telescope", line 11, in
load_entry_point('telescope-ngs==1.0.3', 'console_scripts', 'telescope')()
File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/ main__.py", line 95, in main
args.func(args)
File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/telescope_assign.py", line 216, in run
ts.load_alignment(annot)
File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/utils/model.py", line 164, in load_alignment
self._mapping_to_matrix(maps, scorerange, alninfo)
File "/dartfs-hpc/rc/home/k/f0042dk/.conda/envs/py37/lib/python3.7/site-packages/telescope/utils/model.py", line 339, in _mapping_to_matrix
rownames = np.array(sorted(_ridx, key=_ridx.get))
MemoryError
2020-02-04 09:32:37 INFO
Version: 1.0.3 Input Options samfile: BAM_STAR/ICGC-ABMB-20100303-10-TR.bam gtffile: gencode.v31.annotation.gtf attribute: gene_id no_feature_key: no_feature ncpu: 1 tempdir: None Reporting Options quiet: False debug: False logfile:
I have sufficient RAM. Can you help me with error please? Thank you.