CLAM peakcaller error #33
Description
(clam) scop@wanglab:/data1/seq_analysis/rip_seq/clam$ CLAM peakcaller \
-i /data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/realigned.sorted.bam
-c /data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/unique.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/realigned.sorted.bam
/data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/realigned.sorted.bam
-o /data1/seq_analysis/rip_seq/clam/peaks
--gtf /home/scop/mm39_m34.gtf
-p 32
/home/scop/miniconda3/envs/clam/bin/CLAM:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').run_script('CLAM==1.2.0', 'CLAM')
2025-06-18 15:18:47,063 - CLAM.Peakcaller - INFO -
start
2025-06-18 15:18:47,063 - CLAM.Peakcaller - INFO -
run info: /home/scop/miniconda3/envs/clam/bin/CLAM peakcaller -i /data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/realigned.sorted.bam -c /data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/unique.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/realigned.sorted.bam /data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/realigned.sorted.bam -o /data1/seq_analysis/rip_seq/clam/peaks --gtf /home/scop/mm39_m34.gtf -p 32
2025-06-18 15:18:47,064 - CLAM.Peakcaller - INFO -
Params:
ip_bam_list = ['/data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti1.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti2.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti3.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/anti4.sorted_out/realigned.sorted.bam']
gtf_fp = /home/scop/mm39_m34.gtf
con_bam_list = ['/data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/unique.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg1.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg2.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg3.sorted_out/realigned.sorted.bam', '/data1/seq_analysis/rip_seq/clam/realign_out/igg4.sorted_out/realigned.sorted.bam']
nthread = 32
out_dir = /data1/seq_analysis/rip_seq/clam/peaks
binsize = 50
norm_lib = False
unique_only = False
unstranded = False
qval_cutoff = 0.05
fold_change = [2.0]
min_clip_cov = 4
pooling = False
2025-06-18 15:18:47,064 - CLAM.Peakcaller - INFO -
read GTF from "/home/scop/mm39_m34.gtf"
2025-06-18 15:18:49,613 - CLAM.Peakcaller - INFO -
multi-threading
2025-06-18 15:18:49,975 - CLAM.Peakcaller - DEBUG -
pid 375309 : 0 / 1787 (0.00%)
2025-06-18 15:18:49,998 - CLAM.Peakcaller - DEBUG -
pid 375310 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,100 - CLAM.Peakcaller - DEBUG -
pid 375311 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,121 - CLAM.Peakcaller - DEBUG -
pid 375312 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,183 - CLAM.Peakcaller - DEBUG -
pid 375313 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,234 - CLAM.Peakcaller - DEBUG -
pid 375314 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,278 - CLAM.Peakcaller - DEBUG -
pid 375315 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,362 - CLAM.Peakcaller - DEBUG -
pid 375316 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,422 - CLAM.Peakcaller - DEBUG -
pid 375317 : 0 / 1787 (0.00%)
2025-06-18 15:18:50,487 - CLAM.Peakcaller - DEBUG -
pid 375318 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,552 - CLAM.Peakcaller - DEBUG -
pid 375319 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,577 - CLAM.Peakcaller - DEBUG -
pid 375320 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,631 - CLAM.Peakcaller - DEBUG -
pid 375321 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,727 - CLAM.Peakcaller - DEBUG -
pid 375322 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,812 - CLAM.Peakcaller - DEBUG -
pid 375334 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,834 - CLAM.Peakcaller - DEBUG -
pid 375346 : 0 / 1788 (0.00%)
2025-06-18 15:18:50,933 - CLAM.Peakcaller - DEBUG -
pid 375360 : 0 / 1787 (0.00%)
2025-06-18 15:18:50,978 - CLAM.Peakcaller - DEBUG -
pid 375362 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,053 - CLAM.Peakcaller - DEBUG -
pid 375363 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,090 - CLAM.Peakcaller - DEBUG -
pid 375364 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,137 - CLAM.Peakcaller - DEBUG -
pid 375365 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,226 - CLAM.Peakcaller - DEBUG -
pid 375366 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,239 - CLAM.Peakcaller - DEBUG -
pid 375367 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,281 - CLAM.Peakcaller - DEBUG -
pid 375368 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,326 - CLAM.Peakcaller - DEBUG -
pid 375369 : 0 / 1787 (0.00%)
2025-06-18 15:18:51,371 - CLAM.Peakcaller - DEBUG -
pid 375370 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,413 - CLAM.Peakcaller - DEBUG -
pid 375371 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,461 - CLAM.Peakcaller - DEBUG -
pid 375372 : 0 / 1788 (0.00%)
2025-06-18 15:18:51,502 - CLAM.Peakcaller - DEBUG -
pid 375373 : 0 / 1787 (0.00%)
2025-06-18 15:18:51,540 - CLAM.Peakcaller - DEBUG -
pid 375374 : 0 / 1787 (0.00%)
2025-06-18 15:18:51,617 - CLAM.Peakcaller - DEBUG -
pid 375375 : 0 / 1787 (0.00%)
2025-06-18 15:18:51,626 - CLAM.Peakcaller - DEBUG -
pid 375376 : 0 / 1759 (0.00%)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/scop/miniconda3/envs/clam/lib/python3.12/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/home/scop/miniconda3/envs/clam/lib/python3.12/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/CLAM/peakcaller.py", line 425, in _child_peak_caller
BED += call_gene_peak(bam_dict, gene,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/CLAM/peakcaller.py", line 324, in call_gene_peak
ip_sum = np.apply_along_axis(np.sum, 1, interval_ip)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/numpy-2.3.0-py3.12-linux-x86_64.egg/numpy/lib/_shape_base_impl.py", line 390, in apply_along_axis
raise ValueError(
ValueError: Cannot apply_along_axis when any iteration dimensions are 0
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/scop/miniconda3/envs/clam/bin/CLAM", line 4, in
import('pkg_resources').run_script('CLAM==1.2.0', 'CLAM')
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/pkg_resources/init.py", line 752, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/pkg_resources/init.py", line 1750, in run_script
exec(script_code, namespace, namespace)
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/EGG-INFO/scripts/CLAM", line 329, in
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/EGG-INFO/scripts/CLAM", line 66, in main
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/CLAM/peakcaller.py", line 641, in parser
File "/home/scop/miniconda3/envs/clam/lib/python3.12/site-packages/CLAM-1.2.0-py3.12.egg/CLAM/peakcaller.py", line 592, in peakcaller
File "/home/scop/miniconda3/envs/clam/lib/python3.12/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/scop/miniconda3/envs/clam/lib/python3.12/multiprocessing/pool.py", line 774, in get
raise self._value