I'm trying to run Telescope assign but I get this error. I sorted the bam file based on name and also I tried samtools collate. They both give me this error. I was wondering if you have any idea what could be happening.
Thank you for your time.
2024-01-24 13:28:27 INFO
Version: 1.0.3
Input Options
samfile: /data1/sabina/telescope/bam/H3K4me2_IR01_48b.nodupsort.bam
gtffile: /data1/sabina/telescope/te_pan_gtf/IR01_48b.te_reference.gtf
attribute: locus
no_feature_key: __no_feature
ncpu: 8
tempdir: /tmp/tmpq81tl_44
Reporting Options
quiet: False
debug: False
logfile:
outdir: /data1/sabina/telescope/output
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: 200000
em_epsilon: 1e-07
max_iter: 100
use_likelihood: False
skip_em: False
(from run in telescope_assign.py:197)
2024-01-24 13:28:27 INFO Loading annotation... (from run in telescope_assign.py:205)
2024-01-24 13:28:27 INFO Loaded annotation in 0 minutes and 0 secs (from run in telescope_assign.py:208)
2024-01-24 13:28:27 INFO Loaded 3684 features. (from run in telescope_assign.py:209)
2024-01-24 13:28:27 INFO Loading alignments... (from run in telescope_assign.py:214)
2024-01-24 13:28:27 INFO Loading alignments in parallel... (from _load_parallel in model.py:175)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_1:0-6232260 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_2:0-3836410 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_10:0-1811216 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_11:0-1636465 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_12:0-1426635 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_13:0-1167977 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_16:0-543404 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_20:0-423683 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_19:0-541371 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_21:0-339780 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_3:0-3545279 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_4:0-3013063 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_5:0-2898299 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_6:0-2494635 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_7:0-2855057 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_8:0-2400776 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_9:0-1967252 (from fetch_region in alignment.py:191)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, *kwds))
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(args))
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/alignment.py", line 206, in fetch_region
samiter = sf.fetch(*region, multiple_iterators=True)
File "pysam/libcalignmentfile.pyx", line 1100, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetch called on bamfile without index
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/sabina/mambaforge/envs/telescope/bin/telescope", line 10, in
sys.exit(main())
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/main.py", line 95, in main
args.func(args)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/telescope_assign.py", line 216, in run
ts.load_alignment(annot)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/model.py", line 159, in load_alignment
maps, scorerange, alninfo = self._load_parallel(annotation)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/model.py", line 198, in _load_parallel
for mfile, scorerange, _pxu in result.get():
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: fetch called on bamfile without index
Hello @mlbendall!
I'm trying to run Telescope assign but I get this error. I sorted the bam file based on name and also I tried samtools collate. They both give me this error. I was wondering if you have any idea what could be happening. Thank you for your time.
Command:
telescope assign /data1/sabina/telescope/bam/H3K4me2_IR01_48b.nodupsort.bam /data1/sabina/telescope/te_pan_gtf/IR01_48b.te_reference.gtf --ncpu 8 --outdir /data1/sabina/telescope/output --updated_samOutput:
2024-01-24 13:28:27 INFO Version: 1.0.3 Input Options samfile: /data1/sabina/telescope/bam/H3K4me2_IR01_48b.nodupsort.bam gtffile: /data1/sabina/telescope/te_pan_gtf/IR01_48b.te_reference.gtf attribute: locus no_feature_key: __no_feature ncpu: 8 tempdir: /tmp/tmpq81tl_44 Reporting Options quiet: False debug: False logfile:
outdir: /data1/sabina/telescope/output
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: 200000
em_epsilon: 1e-07
max_iter: 100
use_likelihood: False
skip_em: False
(from run in telescope_assign.py:197)
2024-01-24 13:28:27 INFO Loading annotation... (from run in telescope_assign.py:205)
2024-01-24 13:28:27 INFO Loaded annotation in 0 minutes and 0 secs (from run in telescope_assign.py:208)
2024-01-24 13:28:27 INFO Loaded 3684 features. (from run in telescope_assign.py:209)
2024-01-24 13:28:27 INFO Loading alignments... (from run in telescope_assign.py:214)
2024-01-24 13:28:27 INFO Loading alignments in parallel... (from _load_parallel in model.py:175)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_1:0-6232260 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_2:0-3836410 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_10:0-1811216 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_11:0-1636465 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_12:0-1426635 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_13:0-1167977 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_16:0-543404 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_20:0-423683 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_19:0-541371 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_21:0-339780 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_3:0-3545279 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_4:0-3013063 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_5:0-2898299 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_6:0-2494635 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_7:0-2855057 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_8:0-2400776 (from fetch_region in alignment.py:191)
2024-01-24 13:28:28 INFO processing IR01_48b.chr_9:0-1967252 (from fetch_region in alignment.py:191)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, *kwds))
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(args))
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/alignment.py", line 206, in fetch_region
samiter = sf.fetch(*region, multiple_iterators=True)
File "pysam/libcalignmentfile.pyx", line 1100, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetch called on bamfile without index
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/sabina/mambaforge/envs/telescope/bin/telescope", line 10, in
sys.exit(main())
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/main.py", line 95, in main
args.func(args)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/telescope_assign.py", line 216, in run
ts.load_alignment(annot)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/model.py", line 159, in load_alignment
maps, scorerange, alninfo = self._load_parallel(annotation)
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/site-packages/telescope/utils/model.py", line 198, in _load_parallel
for mfile, scorerange, _pxu in result.get():
File "/home/sabina/mambaforge/envs/telescope/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: fetch called on bamfile without index