Error while running FusionAnnotator

[snashraf]

Hi team,

I am trying to run FusionAnnotator.py on my sample but I am getting below error

(base) SRLM-NAJEEBS:oncoKBAnalysis nsyed$ python3 FusionAnnotator.py -i temp.tsv -o temp_val.tsv -b ${code} INFO:FusionAnnotator:annotating temp.tsv ... Traceback (most recent call last): File "FusionAnnotator.py", line 66, in args.func(args) File "FusionAnnotator.py", line 44, in main cancertypemap, argv.structural_variant_name_format) TypeError: processsv() missing 1 required positional argument: 'nameregex'

I have used latest FusionAnnotator script and tried to run with example with https://github.com/oncokb/oncokb-annotator/blob/master/data/example_fusions.txt as well but still getting same error. Could some one please help me on this ?

Regards, Najeeb

[zhx828]

@snashraf I can running the example script locally. The tests are passing too. Could you do some debugging on your script?

[snashraf]

I am using the script available at GitHub page. Are you using same also ?

Regards Najeeb

On Mon, 10 May 2021, 17:13 Hongxin, @.***> wrote:

@snashraf https://github.com/snashraf I can running the example script locally. The tests are passing too. Could you do some debugging on your script?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-836751506, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBFIN2TAVSJABLP4ZIN6Z3TM7SX3ANCNFSM44QPXEAQ .

[zhx828]

Yup

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---

From: snashraf @.> Sent: Monday, May 10, 2021 1:39:35 PM To: oncokb/oncokb-annotator @.> Cc: Zhang, Hongxin/Sloan Kettering Institute @.>; Comment @.> Subject: [EXTERNAL] Re: [oncokb/oncokb-annotator] Error while running FusionAnnotator (#126)

I am using the script available at GitHub page. Are you using same also ?

Regards Najeeb

On Mon, 10 May 2021, 17:13 Hongxin, @.***> wrote:

@snashraf https://github.com/snashraf I can running the example script locally. The tests are passing too. Could you do some debugging on your script?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-836751506, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBFIN2TAVSJABLP4ZIN6Z3TM7SX3ANCNFSM44QPXEAQ .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-837024498, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABJGQF6AZZO6YLP5GYQKBE3TNAK5PANCNFSM44QPXEAQ.

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[snashraf]

That's weird! 😰😰

Ok thanks ! I will try again.

On Mon, 10 May 2021, 20:41 Hongxin, @.***> wrote:

Yup

Get Outlook for iOShttps://aka.ms/o0ukef

---

From: snashraf @.> Sent: Monday, May 10, 2021 1:39:35 PM To: oncokb/oncokb-annotator @.> Cc: Zhang, Hongxin/Sloan Kettering Institute @.>; Comment @.> Subject: [EXTERNAL] Re: [oncokb/oncokb-annotator] Error while running FusionAnnotator (#126)

I am using the script available at GitHub page. Are you using same also ?

Regards Najeeb

On Mon, 10 May 2021, 17:13 Hongxin, @.***> wrote:

@snashraf https://github.com/snashraf I can running the example script locally. The tests are passing too. Could you do some debugging on your script?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-836751506 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABBFIN2TAVSJABLP4ZIN6Z3TM7SX3ANCNFSM44QPXEAQ

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-837024498>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABJGQF6AZZO6YLP5GYQKBE3TNAK5PANCNFSM44QPXEAQ

.

Only open attachments or links from trusted senders. Report phishing to @. ***

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Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oncokb/oncokb-annotator/issues/126#issuecomment-837027502, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBFIN2RA7U3LTSL3EGT3PTTNALFDANCNFSM44QPXEAQ .

[zhx828]

@snashraf did you figure out what the issue is?