ronin-gw / pymasc Goto Github PK

Hi,

I've tried to test your soft but have an error during process. Only *_stats.tab are created at the end of process.

I install pymasc via pip install.

Here the command I used:
pymasc -p 10 -e * -i I -n test2 -o test2masc processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam

and logs:

[2021-03-16 11:51:30,003 | INFO] PyMaSC.pymasc : PyMaSC version 0.3.2 with Python2.7.18
[2021-03-16 11:51:30,004 | INFO] PyMaSC.pymasc : Make output directory: test2masc
[2021-03-16 11:51:30,103 | INFO] PyMaSC.pymasc : Check read length: Get median from read length distribution
[2021-03-16 11:51:30,103 | INFO] PyMaSC.handler.masc : Check read length... : processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Scan 6,336,378 reads, 1,038,711 reads were unmapped and 4,775,493 reads >= MAPQ 1.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : 6,336,378 reads were paired: 3,168,189 reads were 1st and 3,168,189 reads were last segment.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Note that only 1st reads in the templates will be used for calculation.
[2021-03-16 11:52:47,362 | INFO] PyMaSC.core.readlen : Estimated read length = 150
[2021-03-16 11:52:47,362 | INFO] PyMaSC.pymasc : Calculate cross-correlation between 0 to 1000 base shiftwith reads MAOQ >= 1
[2021-03-16 11:52:47,362 | INFO] PyMaSC.pymasc : Process processed_data/ce11/NGS/ChIPseq/bam/H3k4me1_WThexCtrl_rep1.bwa_aln.sort.bam
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading II reads to bit array...
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading III reads to bit array...
[2021-03-16 11:52:47,398 | INFO] PyMaSC.bacore.mscc : Loading IV reads to bit array...
[2021-03-16 11:52:47,399 | INFO] PyMaSC.bacore.mscc : Loading V reads to bit array...
[2021-03-16 11:52:47,399 | INFO] PyMaSC.bacore.mscc : Loading MtDNA reads to bit array...
[2021-03-16 11:52:47,400 | INFO] PyMaSC.bacore.mscc : Loading X reads to bit array...
[2021-03-16 11:52:47,400 | INFO] PyMaSC.bacore.mscc : Loading I reads to bit array...
[2021-03-16 11:52:47,742 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for MtDNA...
[2021-03-16 11:52:49,955 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for II...
[2021-03-16 11:52:50,131 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for IV...
[2021-03-16 11:52:50,200 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for III...
[2021-03-16 11:52:50,252 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for X...
[2021-03-16 11:52:50,453 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for I...
[2021-03-16 11:52:50,564 | INFO] PyMaSC.bacore.mscc : Calculate cross-correlation for V...
[2021-03-16 11:52:54,707 | WARNING] PyMaSC.handler.result : Whole genome Forward/Reverse read count imbalance.
[2021-03-16 11:52:54,707 | WARNING] PyMaSC.handler.result : +/- = 998928 / 1003500, Chi-squared test p-val = 0.0223354912445 <= 0.05
[2021-03-16 11:52:54,877 | INFO] PyMaSC.output.stats : Output 'test2masc/test2_stats.tab'
[2021-03-16 11:52:54,878 | INFO] PyMaSC.output.table : Output 'test2masc/test2_nreads.tab'
Traceback (most recent call last):
File "/nfs/work/gen2i/technique/tools/bin/pymasc", line 8, in
sys.exit(main())
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/init.py", line 20, in _inner
main_func()
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 98, in main
output_results(args, output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/pymasc.py", line 189, in output_results
output_nreads_table(output_basename, result_handler)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/utils/output.py", line 10, in _io_func
return func(*args, **kwargs)
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 179, in output_nreads_table
with NReadsIO(outfile, 'w') as tab:
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 36, in enter
self.open()
File "/nfs/work/gen2i/technique/tools/lib/python2.7/site-packages/PyMaSC/output/table.py", line 33, in open
self.fp = open(self.path, self.mode, newline='')
TypeError: 'newline' is an invalid keyword argument for this function

I will try with python 3.9.2 version but I'm waiting for the admin of HPC I use to install a devel lib to be able to correctly compile python.

Many thanks,
cheers