stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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macs2 call peak error #1331

Closed VikiyD closed 1 year ago

VikiyD commented 1 year ago

Thanks for providing such a great software, I built r object according to the tutorial (https://stuartlab.org/signac/articles/pbmc_vignette.html). Before normalization, I'm trying to call peaks within my dataset with CallPeaks function. However, I got an error below:

peaks <- CallPeaks(pbmc,outdir ="/signac")
# insert reproducible example here
INFO  @ Fri, 10 Feb 2023 12:29:52: 
# Command line: callpeak -t fragments.tsv.gz -g 2.7e+09 -f BED --nomodel --extsize 200 --shift -100 -n Ctrl --outdir /signac
# ARGUMENTS LIST:
# name = Ctrl
# format = BED
# ChIP-seq file = ['fragments.tsv.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Paired-End mode is off

INFO  @ Fri, 10 Feb 2023 12:29:52: #1 read tag files... 
INFO  @ Fri, 10 Feb 2023 12:29:52: #1 read treatment tags... 
Traceback (most recent call last):
  File "MACS2/IO/Parser.pyx", line 302, in MACS2.IO.Parser.BEDParser.__tlen_parse_line
IndexError: list index out of range
Exception ignored in: 'MACS2.IO.Parser.GenericParser.tsize'
Traceback (most recent call last):
  File "MACS2/IO/Parser.pyx", line 302, in MACS2.IO.Parser.BEDParser.__tlen_parse_line
IndexError: list index out of range
Traceback (most recent call last):
  File "MACS2/IO/Parser.pyx", line 323, in MACS2.IO.Parser.BEDParser.__fw_parse_line
IndexError: list index out of range
valentinaOpazo commented 1 year ago

I got the same error, how do you solve?