x_TEA_main.py: error: no such option: --bamsnap

[sidi-yang]

Dear Simon,

I have run xtea using a case-control mode and got an error like this:

x_TEA_main.py: error: no such option: --bamsnap Usage: x_TEA_main.py [options]

I saw some other issues with the same error here, and just wondering should I ignore this error? Does this error affect the outputs?

Thank you, Sidi

[simoncchu]

Yes, you can ignore these errors. It doesn't affect the results.

[shilpasy]

@simoncchu , sorry to ask you about the same issue. I get the same exact error but I do obtain any results. My vcf files are being generated, but are blank (only header is present in the .vcf file The following temp files are also empty: candidate_disc_filtered_cns_post_filtering.txt.td.tmp, candidate_disc_filtered_cns_post_filtering.txt.orphan.tmp, candidate_disc_filtered_cns_post_filtering.txt.td_sibling.tmp, candidate_disc_filtered_cns_post_filtering_somatic.txt.candidate_somatic_td_cluster_from_ctrl.txt.tmp_clip_chk.txt