DEBUG: Starting telbam generation for 1 inputs
DEBUG: Inline execution of telbam generation, 2 threads per process
Collecting meta-data for all samples | 2023-07-16 14:34:40
[Error] telomerecat stopped unexpectedly, sorry!
Traceback (most recent call last):
File "parabam/core.pyx", line 61, in parabam.core.CmdLineInterface.handle
File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/bam2length.py", line 42, in run_cmd
self.run(
File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/bam2length.py", line 90, in run
length_interface.run(
File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 911, in run
vital_stats = vital_stats_finder.get_vital_stats(sample_path)
File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 447, in get_vital_stats
vital_stats = self.csv_to_dict(vital_stats_csv)
File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 422, in csv_to_dict
min_qual = int(insert_dat["min_qual"])
OverflowError: cannot convert float infinity to integer
I've tried this with a couple of different bam files, get the same result.
Hi,
I am getting the following error when running bam2length
telomerecat bam2length -v2 wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep1V2_telbam.bam telomerecat bam2length has started. Start Time: 2023-07-16 14:34:39
DEBUG: Starting telbam generation for 1 inputs DEBUG: Inline execution of telbam generation, 2 threads per process Collecting meta-data for all samples | 2023-07-16 14:34:40
[Error] telomerecat stopped unexpectedly, sorry! Traceback (most recent call last): File "parabam/core.pyx", line 61, in parabam.core.CmdLineInterface.handle File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/bam2length.py", line 42, in run_cmd self.run( File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/bam2length.py", line 90, in run length_interface.run( File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 911, in run vital_stats = vital_stats_finder.get_vital_stats(sample_path) File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 447, in get_vital_stats vital_stats = self.csv_to_dict(vital_stats_csv) File "/home/jmayer/.local/lib/python3.10/site-packages/telomerecat/telbam2length.py", line 422, in csv_to_dict min_qual = int(insert_dat["min_qual"]) OverflowError: cannot convert float infinity to integer
I've tried this with a couple of different bam files, get the same result.
Thanks,
John