Closed jzluo closed 8 months ago
This is a great bug report, thanks.
Can you show me the line in your input file with 6,351611
?
And also the line with 3516110.016
? pos
is treated as an integer by pheweb, so I don't understand why it wrote out 3516110.016
. That's probably related to the problem.
Could you show me the output of zcat ~/pheweb/generated-by-pheweb/parsed/008_52 | grep "6 351611" | hexdump -C
? Perhaps there are more tabs in there that didn't survive the copy-paste.
Hi, running into an issue I think with parse-input-files:
Please include:
pheweb -h
. If you're not on the latest version, consider upgrading withpip3 install --upgrade
and trying again. PheWeb 1.3.13Child process had exception, info dumped to ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.418222 (Details in ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.431163)
$ cat ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.431163 ======= Exception ==== Child process had exception, info dumped to ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.418222
======= Traceback ==== Traceback (most recent call last): File "/home/jon/.local/lib/python3.7/site-packages/pheweb/command_line.py", line 131, in main run(sys.argv[1:]) File "/home/jon/.local/lib/python3.7/site-packages/pheweb/command_line.py", line 121, in run handlerssubcommand File "/home/jon/.local/lib/python3.7/site-packages/pheweb/command_line.py", line 62, in f module_run(argv) File "/home/jon/.local/lib/python3.7/site-packages/pheweb/load/sites.py", line 63, in run manna.apply_ret(ret) File "/home/jon/.local/lib/python3.7/site-packages/pheweb/load/sites.py", line 100, in apply_ret raise PheWebError('Child process had exception, info dumped to {}'.format(exc_filepath)) pheweb.utils.PheWebError: Child process had exception, info dumped to ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.418222
$ cat ~/pheweb/generated-by-pheweb/tmp/exception-2021-06-08T15-04-24.418222 Child process had exception: (['6', '351611.0', '6.7', '0.00011'], ['chrom', 'pos', 'ref', 'alt', 'pval', 'beta', 'sebeta', 'maf']) Traceback: Traceback (most recent call last): File "/home/jon/.local/lib/python3.7/site-packages/pheweb/load/sites.py", line 131, in mp_target for ret in merge(task['files_to_merge'], task['out_filepath']): File "/home/jon/.local/lib/python3.7/site-packages/pheweb/load/sites.py", line 187, in merge new_v = next(readers[reader_id]) File "/home/jon/.local/lib/python3.7/site-packages/pheweb/file_utils.py", line 169, in _get_variants assert len(unparsed_variant) == len(self._all_fields), (unparsed_variant, self._all_fields) AssertionError: (['6', '351611.0', '6.7', '0.00011'], ['chrom', 'pos', 'ref', 'alt', 'pval', 'beta', 'sebeta', 'maf'])
$ zcat ~/pheweb/generated-by-pheweb/parsed/008_52 | grep "6 351611" 6 35161144 G T 0.026 3.0 1.1 0.00014 6 351611.0 6.7 0.00011 6 3516110.016 .3 0.0 01 0.04
gzip: 008_52: invalid compressed data--format violated
6,331945,C,A,0.7636440987725183,0.000107198,-1.02973,3.42447 6,348277,A,G,0.7509724415781722,0.000260193,-1.01563,3.20025 6,365986,A,G,0.8270841534049443,0.000122692,-1.01508,4.6469
hg_build_number = 38 show_manhattan_filter_consequence = True show_manhattan_filter_button=True