# megaBLAST python wrapper error?

**URL:** <https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155>\
**Category:** usegalaxy.org support\
**Tags:** blast\
**Created:** [December 8, 2022, 11:11pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155 "2022-12-08T23:11:17Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Vanessa\_Corby-Harris](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vanessa_corby-harris/32/3870_2.png) [@Vanessa\_Corby-Harris](https://help.galaxyproject.org/u/Vanessa_Corby-Harris)\
**Post date:** [December 8, 2022, 11:11pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/1 "2022-12-08T23:11:17Z")

</div>

I ran a test file (xxx.txt) containing fasta formatted sequences that I uploaded from my desktop. There are only \<10 sequences in the file. I wanted to test this because I was having issues with running megaBLAST on a larger dataset collection. At any rate, I think there is something happening with this python script that is causing megaBLAST to fail with large or small files.

This was the error message:

File “/project/galaxy/galaxy-py3/galaxy-base/database/shed\_tools/toolshed.g2.bx.psu.edu/repos/devteam/megablast\_wrapper/fb2e0e1dac89/megablast\_wrapper/megablast\_wrapper.py”, line 68  
print megablast\_command  
^  
SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(megablast\_command)?

I also tried to upload a pic of the error screen, not sure if it made it…

 ![error screen](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/17e3ac517fa7d2500fcb38e44803c302890b0da1.jpeg)

This was the input file (for some reason it’s not seeing the \>'s at the start of each sequence title, but they are on there):

> A00129:980:H5TVGDSX2:4:1107:23547:158121:N:0:TGTCGCAT+AAGCTGAC  
> TAGTAGATTTAAAACGAAGGTCTTGGGGGGTGGTACTTCCCTCAATTCCAATAACCTAAAATAAAATTAAAATTAATAAGTATTTAAAATTTAATATTACGCGCTAGCGTAACATCTGACATCCATTTCTTCCCATGTGATAAGGT  
> A00129:980:H5TVGDSX2:4:1114:6777:151701:N:0:TGTCGCAT+AAGCTGAC  
> GTCGGAATGGAATCGTAAATTGGACGGGACTTATACTAAATATTCTAGTCTTACCAGGTATTCTGCATTTTTCCACAGGCACACATGTATCTTTCAAACAATCCGTGAATATAGTGTGAGGCTTTATTCCCTTCTTCCTCATTAACTGAG  
> A00129:980:H5TVGDSX2:4:1124:1524:98311:N:0:TGTCGCAT+AAGCTGAC  
> CACCTAACCTAGAGTACCACTTTAATCGTAACTAAAACTACTCTACTACGGAGCTGAGTCTTTAGAGGCAACTCAACCTTCCTCACATATAAGCTAAAAGTGGTGGTCTAATCCACTCTGCTTTTAGACTCTTATATGCAAGTTCACTCC  
> A00129:980:H5TVGDSX2:4:1126:11279:367461:N:0:TGTCGCAT+AAGCTGAC  
> ACCCCATCCGAATGCCAACTCTAGCGCTTGTTTAGCATTCTCAATGGTTGCTACTCGACGACCCAATCCTCGAGCATGTGTCCAATTGGTTGTTCCTTCTATAGAAACATTATCCAGATTGGCTAGAAACACGGGTCTTGTTGGATGTTT  
> A00129:980:H5TVGDSX2:4:1127:7699:341781:N:0:TGTCGCAT+AAGCTGAC  
> CGGATAAAGGCAAATCAGTAATACCTAACCAAGCTAACCTAATTAACAAACAATTTGAAATTGTATTCAATATGTCCGTTATTGGAGAACCTGATGGAATTCCGCAAGGTACTCGGTACACCAAATCGCGACATAGATGACTAGGCG  
> A00129:980:H5TVGDSX2:4:1140:5041:243771:N:0:TGTCGCAT+AAGCTGAC  
> CCACCGTAACAAACTAGCACGACATGTCTAGAAAATTCGGATAAAGGCAAATCAGTAATACCTTGCCAAGCCAATCGAATTAACAAACAATTCGAAATAGTATTCAAAATGTCCGTAATTGGTGATCCAGAAGGAATACCGCATAGTACG  
> A00129:980:H5TVGDSX2:4:1169:13883:227481:N:0:TGTCGCAT+AAGCTGAC  
> TATATTTTTCTTTCTTACTCCAATTACTTTCTTCTACGGCAAATACAAGTTATTTCATTTCTTTGCGCTTTATAAGTAACCGTTGTAACTTAGTAACTCTTAGTTCGAGGAATTATTTAGAAAGCTTTTTAAGTAACAATATATTT

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<div class="post-metadata">

**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [December 14, 2022, 5:55am UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/2 "2022-12-14T05:55:50Z")

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Hi @Vanessa_Corby-Harris  
I cannot reproduce megablast error on [usegalaxy.org](http://usegalaxy.org). I tested several small query datasets.  
‘\>’ character should be visible on data preview. If it is absent, there is no proper name line.  
Can you run any other tool on the input/query file, for example, convert FASTA to tabular? If yes, recreate the FASTA file using tabular-to-FASTA. Do you see ‘\>’?  
Kind regards,  
Igor

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<div class="post-metadata">

**Author:** ![Vanessa\_Corby-Harris](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vanessa_corby-harris/32/3870_2.png) [@Vanessa\_Corby-Harris](https://help.galaxyproject.org/u/Vanessa_Corby-Harris)\
**Post date:** [December 15, 2022, 9:00pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/3 "2022-12-15T21:00:44Z")

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Hi @igor,

Thank you for answering! I can convert my FASTA to tabular. If I take a file from my collection, the forward reads, I input something that looks like this:

 ![fasta snip](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/d/d353f36a895a1449f28e94ebd1efc80657b2e1c0.jpeg)

and I get something like this:

 ![table snip](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/9/9794b91ecbc07e54b3a00664958dc31c45c64900.jpeg)

I don’t know of a tabular-to-FASTA tool. Is it buried within something else? When I search for that, nothing comes up.

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<div class="post-metadata">

**Author:** ![Vanessa\_Corby-Harris](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vanessa_corby-harris/32/3870_2.png) [@Vanessa\_Corby-Harris](https://help.galaxyproject.org/u/Vanessa_Corby-Harris)\
**Post date:** [December 15, 2022, 9:21pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/4 "2022-12-15T21:21:26Z")

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@igor

Hang on a minute… I might know what is going on.

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<div class="post-metadata">

**Author:** ![Vanessa\_Corby-Harris](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/vanessa_corby-harris/32/3870_2.png) [@Vanessa\_Corby-Harris](https://help.galaxyproject.org/u/Vanessa_Corby-Harris)\
**Post date:** [December 15, 2022, 11:14pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/5 "2022-12-15T23:14:00Z")

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@igor

I was using an old version of megaBLAST (circled in red). I am using the USDA SciNet Galaxy, and this is an option still.

 ![Capture megaBLAST](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/170737e028aa0de0266fa072ecfcf6613c507897.jpeg)

I don’t see it on the [usegalaxy.org](http://usegalaxy.org) (non-USDA SciNet) page. I guess they need to deprecate/retire/take down that option. But I still don’t know why it wouldn’t work correctly. Maybe something associated with that tool needs updating or whatever.

At any rate, thank you for taking time out for this.

V

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<div class="post-metadata">

**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [December 15, 2022, 11:24pm UTC](https://help.galaxyproject.org/t/megablast-python-wrapper-error/9155/6 "2022-12-15T23:24:09Z")

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Hi @Vanessa_Corby-Harris  
maybe contact USDA SciNet Galaxy support team. It looks like a server/local issue.  
Alternatively, copy the query file to a public Galaxy, do Blast search, and copy the results back.  
The procedure:  
on ‘source’ Galaxy click on name of FASTA file. Click at Copy Link (chain) icon.  
activate Upload menu on ‘target’ Galaxy, switch to Paste/Fetch Data tab, paste the link and hit Start.  
Hope that helps.  
Kind regards,  
Igor